The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and DNA recognition sequences to maintain nephron progenitor identity¶
To investigate the transcriptional network regulated by Eya1, the author perform Eya1 ChIP-seq. 80 kidneys from E13.5 Eya1(HA-FLAG) knockin mice were used. The kidneys were homogenized, lysed, and sonicated and purified. After washing, FLAG peptide was usedfor elution. Then generate sequence libraries and sequenced on Illumina NextSeq500.
In [2]:
mkdir -p /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq/
In [2]:
cd /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq/
To download the sra and raw fastq files¶
In [6]:
prefetch SRR19193869 -O /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq
2022-12-01T23:23:51 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-01T23:23:51 prefetch.3.0.0: 1) Downloading 'SRR19193869'... 2022-12-01T23:23:51 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability. 2022-12-01T23:23:51 prefetch.3.0.0: Downloading via HTTPS... 2022-12-01T23:24:17 prefetch.3.0.0: HTTPS download succeed 2022-12-01T23:24:19 prefetch.3.0.0: 'SRR19193869' is valid 2022-12-01T23:24:19 prefetch.3.0.0: 1) 'SRR19193869' was downloaded successfully 2022-12-01T23:24:19 prefetch.3.0.0: 'SRR19193869' has 0 unresolved dependencies
In [13]:
prefetch SRR19193868 -O /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq
2022-12-01T23:36:39 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores. 2022-12-01T23:36:40 prefetch.3.0.0: 1) Downloading 'SRR19193868'... 2022-12-01T23:36:40 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability. 2022-12-01T23:36:40 prefetch.3.0.0: Downloading via HTTPS... 2022-12-01T23:37:32 prefetch.3.0.0: HTTPS download succeed 2022-12-01T23:37:34 prefetch.3.0.0: 'SRR19193868' is valid 2022-12-01T23:37:34 prefetch.3.0.0: 1) 'SRR19193868' was downloaded successfully 2022-12-01T23:37:34 prefetch.3.0.0: 'SRR19193868' has 0 unresolved dependencies
In [7]:
fastq-dump --split-files /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq/SRR19193869/SRR19193869.sra
Rejected 42853510 READS because READLEN < 1 Read 42853510 spots for /mnt/storage/r0823712/jupyternotebooks/assignment2/ChIP-seq/SRR19193869/SRR19193869.sra Written 42853510 spots for /mnt/storage/r0823712/jupyternotebooks/assignment2/ChIP-seq/SRR19193869/SRR19193869.sra
Rejected 42853510 READS because READLEN < 1 => length of second reads is 0 (Single-end) => is ok to use this fastq file
In [14]:
fastq-dump --split-files /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq/SRR19193868/SRR19193868.sra
Rejected 44976090 READS because READLEN < 1 Read 44976090 spots for /mnt/storage/r0823712/jupyternotebooks/assignment2/ChIP-seq/SRR19193868/SRR19193868.sra Written 44976090 spots for /mnt/storage/r0823712/jupyternotebooks/assignment2/ChIP-seq/SRR19193868/SRR19193868.sra
In [17]:
ls -lt *.fastq
-rw-r--r-- 1 r0823712 domain users 8231156148 Dec 2 00:41 SRR19193868.fastq -rw-r--r-- 1 r0823712 domain users 7840601428 Dec 2 00:27 SRR19193869.fastq
Check read quality¶
In [12]:
fastqc SRR19193869.fastq
Started analysis of SRR19193869.fastq Approx 5% complete for SRR19193869.fastq Approx 10% complete for SRR19193869.fastq Approx 15% complete for SRR19193869.fastq Approx 20% complete for SRR19193869.fastq Approx 25% complete for SRR19193869.fastq Approx 30% complete for SRR19193869.fastq Approx 35% complete for SRR19193869.fastq Approx 40% complete for SRR19193869.fastq Approx 45% complete for SRR19193869.fastq Approx 50% complete for SRR19193869.fastq Approx 55% complete for SRR19193869.fastq Approx 60% complete for SRR19193869.fastq Approx 65% complete for SRR19193869.fastq Approx 70% complete for SRR19193869.fastq Approx 75% complete for SRR19193869.fastq Approx 80% complete for SRR19193869.fastq Approx 85% complete for SRR19193869.fastq Approx 90% complete for SRR19193869.fastq Approx 95% complete for SRR19193869.fastq Analysis complete for SRR19193869.fastq
In [16]:
fastqc SRR19193868.fastq
Started analysis of SRR19193868.fastq Approx 5% complete for SRR19193868.fastq Approx 10% complete for SRR19193868.fastq Approx 15% complete for SRR19193868.fastq Approx 20% complete for SRR19193868.fastq Approx 25% complete for SRR19193868.fastq Approx 30% complete for SRR19193868.fastq Approx 35% complete for SRR19193868.fastq Approx 40% complete for SRR19193868.fastq Approx 45% complete for SRR19193868.fastq Approx 50% complete for SRR19193868.fastq Approx 55% complete for SRR19193868.fastq Approx 60% complete for SRR19193868.fastq Approx 65% complete for SRR19193868.fastq Approx 70% complete for SRR19193868.fastq Approx 75% complete for SRR19193868.fastq Approx 80% complete for SRR19193868.fastq Approx 85% complete for SRR19193868.fastq Approx 90% complete for SRR19193868.fastq Approx 95% complete for SRR19193868.fastq Analysis complete for SRR19193868.fastq
In [18]:
ls -lt | head
total 15697148 -rw-r--r-- 1 r0823712 domain users 663787 Dec 2 00:44 SRR19193868_fastqc.html -rw-r--r-- 1 r0823712 domain users 381822 Dec 2 00:44 SRR19193868_fastqc.zip -rw-r--r-- 1 r0823712 domain users 8231156148 Dec 2 00:41 SRR19193868.fastq drwxr-xr-x 2 r0823712 domain users 37 Dec 2 00:37 SRR19193868 -rw-r--r-- 1 r0823712 domain users 674349 Dec 2 00:35 SRR19193869_fastqc.html -rw-r--r-- 1 r0823712 domain users 386461 Dec 2 00:35 SRR19193869_fastqc.zip -rw-r--r-- 1 r0823712 domain users 7840601428 Dec 2 00:27 SRR19193869.fastq drwxr-xr-x 2 r0823712 domain users 37 Dec 2 00:24 SRR19193869
In [19]:
wc SRR19193869.fastq
wc SRR19193868.fastq
171414040 342828080 7840601428 SRR19193869.fastq 179904360 359808720 8231156148 SRR19193868.fastq
quality is ok
Alignment of Eya1 ChIP-seq reads¶
In [22]:
bowtie2 -x /mnt/storage/data/resources/genomes/mm10/bowtie2/mm10 SRR19193868.fastq -S ChIP_Eya1.sam
44976090 reads; of these:
44976090 (100.00%) were unpaired; of these:
1246965 (2.77%) aligned 0 times
32314194 (71.85%) aligned exactly 1 time
11414931 (25.38%) aligned >1 times
97.23% overall alignment rate
In [23]:
#Check a couple of lines in the SAM file
head -500 ChIP_Eya1.sam | tail -5
SRR19193868.428 16 chr19 10025990 42 50M * 0 0 TCTATTATGCCTGGACTATTTGTAGACTCTTCCTGCCTGCTGAGGCCTGN IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDD<# AS:i:-1 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:49G0 YT:Z:UU SRR19193868.429 0 chr12 52150953 42 50M * 0 0 CACCTCCACTGTCACCTCCACTGCCACCTCCACTGCCACTGCCACCTCCA DDDDBHHHIGEHHCHHIIIIIECHC1GEHHHF?@GHFHHHIIGHHIIHCC AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU SRR19193868.430 16 chr10 50503366 42 50M * 0 0 GCAATGAAAAGAGTGTGTACAATTACATCCTAGAGTCAGTTCATCTAGTN IIIIIIIIIIIIIIIIIIIIIHIIHIIIIIIIHGIIIIIIIIIIIDD<<# AS:i:-1 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:49C0 YT:Z:UU SRR19193868.431 4 * 0 0 * * 0 0 NCCTTCTGTGGGCATTTCCCATTTTTCAGGTTTTTTAGTGATTTCGTAGA #<<DDIIIIIIIIIIIIIIIIIIIIHIIIIHGHIIIIIIIIIIIIIIIIH YT:Z:UU SRR19193868.432 16 chr15 58867315 42 50M * 0 0 TGGACCCCAGCAGTCAGTAGACCAAGAGTGAAGCTCAACTAGGGGCTGTN IIHIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDD<# AS:i:-1 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:49C0 YT:Z:UU
In [24]:
#Convert the SAM file to BAM format (binary)
samtools view -S -b ChIP_Eya1.sam > ChIP_Eya1.bam
In [25]:
samtools view -c ChIP_Eya1.bam
#-c: count
44976090
In [26]:
# Number of mapped reads.(only one position)
samtools view -c -F 260 ChIP_Eya1.bam
#unmapped reads and not primary alignment would be removed
43729125
In [27]:
samtools sort -O bam -o ChIP_Eya1.sorted.bam ChIP_Eya1.bam
[bam_sort_core] merging from 11 files and 1 in-memory blocks...
In [30]:
samtools index ChIP_Eya1.sorted.bam
In [29]:
ls
ChIP_Eya1.bam SRR19193868 SRR19193869 ChIP_Eya1.sam SRR19193868.fastq SRR19193869.fastq ChIP_Eya1.sorted.bam SRR19193868_fastqc.html SRR19193869_fastqc.html ChIP_Eya1.sorted.bam.bai SRR19193868_fastqc.zip SRR19193869_fastqc.zip
Alignment of the control data ("input")¶
In [20]:
bowtie2 -x /mnt/storage/data/resources/genomes/mm10/bowtie2/mm10 SRR19193869.fastq -S ChIP_input.sam
#-x: index
42853510 reads; of these:
42853510 (100.00%) were unpaired; of these:
1174124 (2.74%) aligned 0 times
31783035 (74.17%) aligned exactly 1 time
9896351 (23.09%) aligned >1 times
97.26% overall alignment rate
In [30]:
samtools view -S -b ChIP_input.sam > ChIP_input.bam
In [31]:
samtools sort -O bam -o ChIP_input.sorted.bam ChIP_input.bam
[bam_sort_core] merging from 10 files and 1 in-memory blocks...
In [29]:
samtools index ChIP_input.sorted.bam
BAM file in IGV¶
REST is a target gene of Eya1, located on chr5. A peak near 5' UTR of the two REST isoforms.
Genome-wide coverage plots¶
In [33]:
# generate a bigwig file that contains only the coverage of the reads
bamCoverage -b ChIP_Eya1.sorted.bam --normalizeUsing RPGC --effectiveGenomeSize 2652783500 -o ChIP_Eya1.bw -bs 5
#RPGC = reads per genomic content (1x normalization); Mapped reads are considered after blacklist filtering (if applied).
#-bs: per how many bins I want to calculated in my bigwig
normalization: 1x (effective genome size 2652783500) bamFilesList: ['ChIP_Eya1.sorted.bam'] binLength: 5 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 5 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000
Peak calling¶
Another example of a target gene, Zfx, located on X chromosome. Peaks in the intron and 3'UTR of the Zfx isoforms.
Peak calling with MACS2¶
MACS can distinguish true, bona fide peaks, from artifacts.
In [14]:
macs2 callpeak -t ChIP_Eya1.sorted.bam -c ChIP_input.sorted.bam -n Eya1 -g 2652783500 -q 0.05
#-t: real ChIP data
#-c: control = input
#-n: output file name
#-g: genome size
#-q: threshold for the peaks (less strengen => more peaks)
# If q=0.05, get many peaks => still can do motif analysis on the top peaks based on fold change or q-value
INFO @ Fri, 02 Dec 2022 23:23:17: # Command line: callpeak -t ChIP_Eya1.sorted.bam -c ChIP_input.sorted.bam -n Eya1 -g 2652783500 -q 0.05 # ARGUMENTS LIST: # name = Eya1 # format = AUTO # ChIP-seq file = ['ChIP_Eya1.sorted.bam'] # control file = ['ChIP_input.sorted.bam'] # effective genome size = 2.65e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 5.00e-02 # The maximum gap between significant sites is assigned as the read length/tag size. # The minimum length of peaks is assigned as the predicted fragment length "d". # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 02 Dec 2022 23:23:17: #1 read tag files... INFO @ Fri, 02 Dec 2022 23:23:17: #1 read treatment tags... INFO @ Fri, 02 Dec 2022 23:23:17: Detected format is: BAM INFO @ Fri, 02 Dec 2022 23:23:17: * Input file is gzipped. INFO @ Fri, 02 Dec 2022 23:23:19: 1000000 INFO @ Fri, 02 Dec 2022 23:23:21: 2000000 INFO @ Fri, 02 Dec 2022 23:23:24: 3000000 INFO @ Fri, 02 Dec 2022 23:23:26: 4000000 INFO @ Fri, 02 Dec 2022 23:23:28: 5000000 INFO @ Fri, 02 Dec 2022 23:23:30: 6000000 INFO @ Fri, 02 Dec 2022 23:23:32: 7000000 INFO @ Fri, 02 Dec 2022 23:23:34: 8000000 INFO @ Fri, 02 Dec 2022 23:23:36: 9000000 INFO @ Fri, 02 Dec 2022 23:23:38: 10000000 INFO @ Fri, 02 Dec 2022 23:23:41: 11000000 INFO @ Fri, 02 Dec 2022 23:23:43: 12000000 INFO @ Fri, 02 Dec 2022 23:23:45: 13000000 INFO @ Fri, 02 Dec 2022 23:23:47: 14000000 INFO @ Fri, 02 Dec 2022 23:23:49: 15000000 INFO @ Fri, 02 Dec 2022 23:23:51: 16000000 INFO @ Fri, 02 Dec 2022 23:23:53: 17000000 INFO @ Fri, 02 Dec 2022 23:23:56: 18000000 INFO @ Fri, 02 Dec 2022 23:23:58: 19000000 INFO @ Fri, 02 Dec 2022 23:24:00: 20000000 INFO @ Fri, 02 Dec 2022 23:24:02: 21000000 INFO @ Fri, 02 Dec 2022 23:24:04: 22000000 INFO @ Fri, 02 Dec 2022 23:24:06: 23000000 INFO @ Fri, 02 Dec 2022 23:24:08: 24000000 INFO @ Fri, 02 Dec 2022 23:24:10: 25000000 INFO @ Fri, 02 Dec 2022 23:24:13: 26000000 INFO @ Fri, 02 Dec 2022 23:24:15: 27000000 INFO @ Fri, 02 Dec 2022 23:24:17: 28000000 INFO @ Fri, 02 Dec 2022 23:24:19: 29000000 INFO @ Fri, 02 Dec 2022 23:24:21: 30000000 INFO @ Fri, 02 Dec 2022 23:24:23: 31000000 INFO @ Fri, 02 Dec 2022 23:24:26: 32000000 INFO @ Fri, 02 Dec 2022 23:24:28: 33000000 INFO @ Fri, 02 Dec 2022 23:24:30: 34000000 INFO @ Fri, 02 Dec 2022 23:24:32: 35000000 INFO @ Fri, 02 Dec 2022 23:24:34: 36000000 INFO @ Fri, 02 Dec 2022 23:24:36: 37000000 INFO @ Fri, 02 Dec 2022 23:24:38: 38000000 INFO @ Fri, 02 Dec 2022 23:24:41: 39000000 INFO @ Fri, 02 Dec 2022 23:24:43: 40000000 INFO @ Fri, 02 Dec 2022 23:24:45: 41000000 INFO @ Fri, 02 Dec 2022 23:24:47: 42000000 INFO @ Fri, 02 Dec 2022 23:24:49: 43000000 INFO @ Fri, 02 Dec 2022 23:24:51: 44000000 INFO @ Fri, 02 Dec 2022 23:24:53: #1.2 read input tags... INFO @ Fri, 02 Dec 2022 23:24:53: Detected format is: BAM INFO @ Fri, 02 Dec 2022 23:24:53: * Input file is gzipped. INFO @ Fri, 02 Dec 2022 23:24:55: 1000000 INFO @ Fri, 02 Dec 2022 23:24:57: 2000000 INFO @ Fri, 02 Dec 2022 23:24:59: 3000000 INFO @ Fri, 02 Dec 2022 23:25:01: 4000000 INFO @ Fri, 02 Dec 2022 23:25:03: 5000000 INFO @ Fri, 02 Dec 2022 23:25:05: 6000000 INFO @ Fri, 02 Dec 2022 23:25:07: 7000000 INFO @ Fri, 02 Dec 2022 23:25:09: 8000000 INFO @ Fri, 02 Dec 2022 23:25:11: 9000000 INFO @ Fri, 02 Dec 2022 23:25:14: 10000000 INFO @ Fri, 02 Dec 2022 23:25:16: 11000000 INFO @ Fri, 02 Dec 2022 23:25:18: 12000000 INFO @ Fri, 02 Dec 2022 23:25:20: 13000000 INFO @ Fri, 02 Dec 2022 23:25:22: 14000000 INFO @ Fri, 02 Dec 2022 23:25:24: 15000000 INFO @ Fri, 02 Dec 2022 23:25:26: 16000000 INFO @ Fri, 02 Dec 2022 23:25:28: 17000000 INFO @ Fri, 02 Dec 2022 23:25:30: 18000000 INFO @ Fri, 02 Dec 2022 23:25:32: 19000000 INFO @ Fri, 02 Dec 2022 23:25:34: 20000000 INFO @ Fri, 02 Dec 2022 23:25:37: 21000000 INFO @ Fri, 02 Dec 2022 23:25:39: 22000000 INFO @ Fri, 02 Dec 2022 23:25:41: 23000000 INFO @ Fri, 02 Dec 2022 23:25:43: 24000000 INFO @ Fri, 02 Dec 2022 23:25:45: 25000000 INFO @ Fri, 02 Dec 2022 23:25:47: 26000000 INFO @ Fri, 02 Dec 2022 23:25:49: 27000000 INFO @ Fri, 02 Dec 2022 23:25:51: 28000000 INFO @ Fri, 02 Dec 2022 23:25:53: 29000000 INFO @ Fri, 02 Dec 2022 23:25:55: 30000000 INFO @ Fri, 02 Dec 2022 23:25:57: 31000000 INFO @ Fri, 02 Dec 2022 23:25:59: 32000000 INFO @ Fri, 02 Dec 2022 23:26:01: 33000000 INFO @ Fri, 02 Dec 2022 23:26:03: 34000000 INFO @ Fri, 02 Dec 2022 23:26:06: 35000000 INFO @ Fri, 02 Dec 2022 23:26:08: 36000000 INFO @ Fri, 02 Dec 2022 23:26:10: 37000000 INFO @ Fri, 02 Dec 2022 23:26:12: 38000000 INFO @ Fri, 02 Dec 2022 23:26:14: 39000000 INFO @ Fri, 02 Dec 2022 23:26:16: 40000000 INFO @ Fri, 02 Dec 2022 23:26:18: 41000000 INFO @ Fri, 02 Dec 2022 23:26:20: 42000000 INFO @ Fri, 02 Dec 2022 23:26:21: #1 tag size is determined as 50 bps INFO @ Fri, 02 Dec 2022 23:26:21: #1 tag size = 50.0 INFO @ Fri, 02 Dec 2022 23:26:21: #1 total tags in treatment: 43729125 INFO @ Fri, 02 Dec 2022 23:26:21: #1 user defined the maximum tags... INFO @ Fri, 02 Dec 2022 23:26:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 02 Dec 2022 23:26:22: #1 tags after filtering in treatment: 40711860 INFO @ Fri, 02 Dec 2022 23:26:22: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 02 Dec 2022 23:26:22: #1 total tags in control: 41679386 INFO @ Fri, 02 Dec 2022 23:26:22: #1 user defined the maximum tags... INFO @ Fri, 02 Dec 2022 23:26:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 02 Dec 2022 23:26:23: #1 tags after filtering in control: 39821414 INFO @ Fri, 02 Dec 2022 23:26:23: #1 Redundant rate of control: 0.04 INFO @ Fri, 02 Dec 2022 23:26:23: #1 finished! INFO @ Fri, 02 Dec 2022 23:26:23: #2 Build Peak Model... INFO @ Fri, 02 Dec 2022 23:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 02 Dec 2022 23:26:26: #2 number of paired peaks: 4574 INFO @ Fri, 02 Dec 2022 23:26:26: start model_add_line... INFO @ Fri, 02 Dec 2022 23:26:27: start X-correlation... INFO @ Fri, 02 Dec 2022 23:26:27: end of X-cor INFO @ Fri, 02 Dec 2022 23:26:27: #2 finished! INFO @ Fri, 02 Dec 2022 23:26:27: #2 predicted fragment length is 73 bps INFO @ Fri, 02 Dec 2022 23:26:27: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 02 Dec 2022 23:26:27: #2.2 Generate R script for model : Eya1_model.r WARNING @ Fri, 02 Dec 2022 23:26:27: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 02 Dec 2022 23:26:27: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 02 Dec 2022 23:26:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 02 Dec 2022 23:26:27: #3 Call peaks... INFO @ Fri, 02 Dec 2022 23:26:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 02 Dec 2022 23:29:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Dec 2022 02:10:30: #4 Write output xls file... Eya1_peaks.xls INFO @ Sat, 03 Dec 2022 02:10:30: #4 Write peak in narrowPeak format file... Eya1_peaks.narrowPeak INFO @ Sat, 03 Dec 2022 02:10:30: #4 Write summits bed file... Eya1_summits.bed INFO @ Sat, 03 Dec 2022 02:10:30: Done!
The uppe result show:\ WARNING Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!
Maybe bad antibody or bad library prepareation cause poor ChIP quality.
In [3]:
macs2 callpeak -t ChIP_Eya1.sorted.bam -c ChIP_input.sorted.bam -n Eya1 -g 2652783500 -q 0.05 --nomodel --extsize 73
#-t: real ChIP data
#-c: control = input
#-n: output file name
#-g: genome size
#-q: threshold for the peaks (less strengen => more peaks)
# If q=0.05, get many peaks => still can do motif analysis on the top peaks based on fold change or q-value
INFO @ Fri, 02 Dec 2022 19:45:14: # Command line: callpeak -t ChIP_Eya1.sorted.bam -c ChIP_input.sorted.bam -n Eya1 -g 2652783500 -q 0.05 --nomodel --extsize 73 # ARGUMENTS LIST: # name = Eya1 # format = AUTO # ChIP-seq file = ['ChIP_Eya1.sorted.bam'] # control file = ['ChIP_input.sorted.bam'] # effective genome size = 2.65e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 5.00e-02 # The maximum gap between significant sites is assigned as the read length/tag size. # The minimum length of peaks is assigned as the predicted fragment length "d". # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 02 Dec 2022 19:45:14: #1 read tag files... INFO @ Fri, 02 Dec 2022 19:45:14: #1 read treatment tags... INFO @ Fri, 02 Dec 2022 19:45:14: Detected format is: BAM INFO @ Fri, 02 Dec 2022 19:45:14: * Input file is gzipped. INFO @ Fri, 02 Dec 2022 19:45:17: 1000000 INFO @ Fri, 02 Dec 2022 19:45:19: 2000000 INFO @ Fri, 02 Dec 2022 19:45:21: 3000000 INFO @ Fri, 02 Dec 2022 19:45:23: 4000000 INFO @ Fri, 02 Dec 2022 19:45:25: 5000000 INFO @ Fri, 02 Dec 2022 19:45:27: 6000000 INFO @ Fri, 02 Dec 2022 19:45:29: 7000000 INFO @ Fri, 02 Dec 2022 19:45:31: 8000000 INFO @ Fri, 02 Dec 2022 19:45:33: 9000000 INFO @ Fri, 02 Dec 2022 19:45:36: 10000000 INFO @ Fri, 02 Dec 2022 19:45:38: 11000000 INFO @ Fri, 02 Dec 2022 19:45:40: 12000000 INFO @ Fri, 02 Dec 2022 19:45:42: 13000000 INFO @ Fri, 02 Dec 2022 19:45:44: 14000000 INFO @ Fri, 02 Dec 2022 19:45:46: 15000000 INFO @ Fri, 02 Dec 2022 19:45:48: 16000000 INFO @ Fri, 02 Dec 2022 19:45:50: 17000000 INFO @ Fri, 02 Dec 2022 19:45:52: 18000000 INFO @ Fri, 02 Dec 2022 19:45:55: 19000000 INFO @ Fri, 02 Dec 2022 19:45:57: 20000000 INFO @ Fri, 02 Dec 2022 19:45:59: 21000000 INFO @ Fri, 02 Dec 2022 19:46:01: 22000000 INFO @ Fri, 02 Dec 2022 19:46:03: 23000000 INFO @ Fri, 02 Dec 2022 19:46:05: 24000000 INFO @ Fri, 02 Dec 2022 19:46:07: 25000000 INFO @ Fri, 02 Dec 2022 19:46:09: 26000000 INFO @ Fri, 02 Dec 2022 19:46:11: 27000000 INFO @ Fri, 02 Dec 2022 19:46:13: 28000000 INFO @ Fri, 02 Dec 2022 19:46:16: 29000000 INFO @ Fri, 02 Dec 2022 19:46:18: 30000000 INFO @ Fri, 02 Dec 2022 19:46:20: 31000000 INFO @ Fri, 02 Dec 2022 19:46:22: 32000000 INFO @ Fri, 02 Dec 2022 19:46:24: 33000000 INFO @ Fri, 02 Dec 2022 19:46:26: 34000000 INFO @ Fri, 02 Dec 2022 19:46:28: 35000000 INFO @ Fri, 02 Dec 2022 19:46:30: 36000000 INFO @ Fri, 02 Dec 2022 19:46:32: 37000000 INFO @ Fri, 02 Dec 2022 19:46:34: 38000000 INFO @ Fri, 02 Dec 2022 19:46:36: 39000000 INFO @ Fri, 02 Dec 2022 19:46:38: 40000000 INFO @ Fri, 02 Dec 2022 19:46:41: 41000000 INFO @ Fri, 02 Dec 2022 19:46:43: 42000000 INFO @ Fri, 02 Dec 2022 19:46:45: 43000000 INFO @ Fri, 02 Dec 2022 19:46:47: 44000000 INFO @ Fri, 02 Dec 2022 19:46:48: #1.2 read input tags... INFO @ Fri, 02 Dec 2022 19:46:48: Detected format is: BAM INFO @ Fri, 02 Dec 2022 19:46:48: * Input file is gzipped. INFO @ Fri, 02 Dec 2022 19:46:50: 1000000 INFO @ Fri, 02 Dec 2022 19:46:53: 2000000 INFO @ Fri, 02 Dec 2022 19:46:55: 3000000 INFO @ Fri, 02 Dec 2022 19:46:57: 4000000 INFO @ Fri, 02 Dec 2022 19:46:59: 5000000 INFO @ Fri, 02 Dec 2022 19:47:01: 6000000 INFO @ Fri, 02 Dec 2022 19:47:03: 7000000 INFO @ Fri, 02 Dec 2022 19:47:05: 8000000 INFO @ Fri, 02 Dec 2022 19:47:07: 9000000 INFO @ Fri, 02 Dec 2022 19:47:09: 10000000 INFO @ Fri, 02 Dec 2022 19:47:11: 11000000 INFO @ Fri, 02 Dec 2022 19:47:13: 12000000 INFO @ Fri, 02 Dec 2022 19:47:15: 13000000 INFO @ Fri, 02 Dec 2022 19:47:17: 14000000 INFO @ Fri, 02 Dec 2022 19:47:19: 15000000 INFO @ Fri, 02 Dec 2022 19:47:21: 16000000 INFO @ Fri, 02 Dec 2022 19:47:23: 17000000 INFO @ Fri, 02 Dec 2022 19:47:26: 18000000 INFO @ Fri, 02 Dec 2022 19:47:28: 19000000 INFO @ Fri, 02 Dec 2022 19:47:30: 20000000 INFO @ Fri, 02 Dec 2022 19:47:32: 21000000 INFO @ Fri, 02 Dec 2022 19:47:34: 22000000 INFO @ Fri, 02 Dec 2022 19:47:36: 23000000 INFO @ Fri, 02 Dec 2022 19:47:38: 24000000 INFO @ Fri, 02 Dec 2022 19:47:40: 25000000 INFO @ Fri, 02 Dec 2022 19:47:42: 26000000 INFO @ Fri, 02 Dec 2022 19:47:44: 27000000 INFO @ Fri, 02 Dec 2022 19:47:46: 28000000 INFO @ Fri, 02 Dec 2022 19:47:48: 29000000 INFO @ Fri, 02 Dec 2022 19:47:50: 30000000 INFO @ Fri, 02 Dec 2022 19:47:52: 31000000 INFO @ Fri, 02 Dec 2022 19:47:54: 32000000 INFO @ Fri, 02 Dec 2022 19:47:56: 33000000 INFO @ Fri, 02 Dec 2022 19:47:58: 34000000 INFO @ Fri, 02 Dec 2022 19:48:00: 35000000 INFO @ Fri, 02 Dec 2022 19:48:03: 36000000 INFO @ Fri, 02 Dec 2022 19:48:05: 37000000 INFO @ Fri, 02 Dec 2022 19:48:07: 38000000 INFO @ Fri, 02 Dec 2022 19:48:09: 39000000 INFO @ Fri, 02 Dec 2022 19:48:11: 40000000 INFO @ Fri, 02 Dec 2022 19:48:13: 41000000 INFO @ Fri, 02 Dec 2022 19:48:15: 42000000 INFO @ Fri, 02 Dec 2022 19:48:16: #1 tag size is determined as 50 bps INFO @ Fri, 02 Dec 2022 19:48:16: #1 tag size = 50.0 INFO @ Fri, 02 Dec 2022 19:48:16: #1 total tags in treatment: 43729125 INFO @ Fri, 02 Dec 2022 19:48:16: #1 user defined the maximum tags... INFO @ Fri, 02 Dec 2022 19:48:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 02 Dec 2022 19:48:17: #1 tags after filtering in treatment: 40711860 INFO @ Fri, 02 Dec 2022 19:48:17: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 02 Dec 2022 19:48:17: #1 total tags in control: 41679386 INFO @ Fri, 02 Dec 2022 19:48:17: #1 user defined the maximum tags... INFO @ Fri, 02 Dec 2022 19:48:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 02 Dec 2022 19:48:17: #1 tags after filtering in control: 39821414 INFO @ Fri, 02 Dec 2022 19:48:17: #1 Redundant rate of control: 0.04 INFO @ Fri, 02 Dec 2022 19:48:17: #1 finished! INFO @ Fri, 02 Dec 2022 19:48:17: #2 Build Peak Model... INFO @ Fri, 02 Dec 2022 19:48:17: #2 Skipped... INFO @ Fri, 02 Dec 2022 19:48:17: #2 Use 73 as fragment length INFO @ Fri, 02 Dec 2022 19:48:17: #3 Call peaks... INFO @ Fri, 02 Dec 2022 19:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 02 Dec 2022 19:51:13: #3 Call peaks for each chromosome... INFO @ Fri, 02 Dec 2022 22:36:05: #4 Write output xls file... Eya1_peaks.xls INFO @ Fri, 02 Dec 2022 22:36:05: #4 Write peak in narrowPeak format file... Eya1_peaks.narrowPeak INFO @ Fri, 02 Dec 2022 22:36:05: #4 Write summits bed file... Eya1_summits.bed INFO @ Fri, 02 Dec 2022 22:36:05: Done!
In [15]:
ls -lt | head -5
total 41625352 -rw-r--r-- 1 r0823712 domain users 195259 Dec 3 02:10 Eya1_summits.bed -rw-r--r-- 1 r0823712 domain users 299027 Dec 3 02:10 Eya1_peaks.narrowPeak -rw-r--r-- 1 r0823712 domain users 344252 Dec 3 02:10 Eya1_peaks.xls -rw-r--r-- 1 r0823712 domain users 99105 Dec 2 23:26 Eya1_model.r
In [16]:
cat Eya1_peaks.narrowPeak | sort -k9 -g -r | head -1000
#-k9: column 9 => -log10(qvalue) => use this to rank peaks
#-g: general format
#-r: reverse / decending on column 9
chr9 21950193 21950730 Eya1_peak_3907 1617 . 50.25843 171.22057 161.78474 344 chr15 72568544 72568871 Eya1_peak_1391 1436 . 42.95110 151.40498 143.65936 191 chr13 54970758 54971192 Eya1_peak_1104 1322 . 42.12254 139.63551 132.26416 294 chr12 42972811 42973228 Eya1_peak_893 1307 . 29.34931 138.06731 130.72491 148 chr2 34090652 34090884 Eya1_peak_2140 1264 . 40.58866 133.59843 126.41547 114 chr18 25668104 25668408 Eya1_peak_1844 1257 . 42.11032 132.84566 125.70210 156 chr15 84829444 84829795 Eya1_peak_1442 1229 . 39.17722 130.03612 122.99651 167 chr15 76521887 76522503 Eya1_peak_1403 1190 . 38.11805 125.98075 119.04048 376 chr2 33018083 33018377 Eya1_peak_2136 1167 . 32.61156 123.64287 116.77760 149 chr4 140258965 140259346 Eya1_peak_2840 1166 . 30.88234 123.47452 116.61620 164 chr4 151604517 151605412 Eya1_peak_2863 1058 . 35.54206 112.49866 105.84244 593 chr12 55600100 55600522 Eya1_peak_908 1034 . 35.36379 110.07584 103.46088 272 chr15 72689744 72690132 Eya1_peak_1392 955 . 28.04696 102.09212 95.59831 234 chr19 4988970 4989348 Eya1_peak_1955 944 . 20.34944 100.88608 94.40835 199 chr11 55607773 55608073 Eya1_peak_547 930 . 30.51480 99.53233 93.06360 156 chr11 118584817 118585200 Eya1_peak_832 923 . 31.27474 98.83235 92.38107 171 chr13 54750797 54751180 Eya1_peak_1100 906 . 28.05319 97.09444 90.67398 115 chr12 24425046 24425369 Eya1_peak_879 877 . 32.04288 94.07970 87.70155 132 chr8 84947106 84947546 Eya1_peak_3780 869 . 26.03490 93.30011 86.94456 245 chr8 14072571 14072895 Eya1_peak_3696 848 . 18.98006 91.16124 84.83669 181 chr2 157913186 157913670 Eya1_peak_2349 842 . 26.66822 90.58193 84.27095 352 chr6 121473009 121473450 Eya1_peak_3358 829 . 25.43862 89.25431 82.95869 270 chr2 153032233 153032552 Eya1_peak_2311 813 . 25.11258 87.67437 81.39782 176 chr7 6410075 6410420 Eya1_peak_3401 800 . 20.79069 86.28214 80.02242 191 chr4 136924579 136924844 Eya1_peak_2826 795 . 27.26839 85.80926 79.55814 130 chr3 113090980 113091200 Eya1_peak_2548 755 . 29.41286 81.74967 75.56110 115 chr7 24359377 24359579 Eya1_peak_3427 737 . 27.76293 79.90568 73.74100 72 chr14 63681555 63681840 Eya1_peak_1297 736 . 25.53131 79.84361 73.68126 108 chr19 42255857 42256209 Eya1_peak_2033 725 . 27.06226 78.70650 72.55489 206 chr5 112718668 112718984 Eya1_peak_3032 721 . 23.15632 78.31824 72.17134 153 chr9 4138911 4139207 Eya1_peak_3890 711 . 26.23463 77.28186 71.15418 124 chr2 39806783 39807118 Eya1_peak_2156 706 . 22.83028 76.78024 70.65681 123 chr16 95093832 95094079 Eya1_peak_1608 630 . 24.18577 69.10124 63.08654 123 chr17 21801453 21801722 Eya1_peak_1644 619 . 25.67922 67.99183 61.98738 145 chr5 33438278 33438516 Eya1_peak_2924 618 . 25.60002 67.85880 61.85963 105 chr9 87021731 87021947 Eya1_peak_4038 612 . 24.69336 67.23691 61.24576 93 chr11 103920708 103921013 Eya1_peak_776 611 . 25.16314 67.12453 61.13711 140 chr7 60974266 60974421 Eya1_peak_3504 603 . 25.21251 66.30712 60.32706 85 chr4 134020693 134020964 Eya1_peak_2811 602 . 20.54798 66.19703 60.22091 142 chr1 173361728 173361968 Eya1_peak_188 586 . 24.74581 64.63068 58.68313 143 chr18 82418879 82419138 Eya1_peak_1934 579 . 23.25796 63.90534 57.96687 125 chr4 131115341 131115587 Eya1_peak_2793 574 . 14.67630 63.41300 57.48396 126 chr9 20857160 20857410 Eya1_peak_3902 573 . 19.89590 63.23513 57.30730 132 chr2 23291134 23291439 Eya1_peak_2090 548 . 22.41256 60.70183 54.81893 91 chr4 152799446 152799805 Eya1_peak_2872 542 . 22.55920 60.07499 54.20254 160 chr4 127173606 127173795 Eya1_peak_2771 532 . 21.98986 59.11264 53.25558 107 chr2 38418040 38418332 Eya1_peak_2151 513 . 15.65552 57.19809 51.37165 113 chr15 74076016 74076321 Eya1_peak_1397 509 . 22.11723 56.73942 50.91861 92 chr14 64568660 64568878 Eya1_peak_1300 495 . 20.28716 55.35202 49.54937 103 chr4 151288930 151289470 Eya1_peak_2862 477 . 20.21166 53.53451 47.75451 224 chr17 56242073 56242333 Eya1_peak_1761 462 . 14.67739 51.97838 46.21926 84 chr9 108826579 108827252 Eya1_peak_4099 456 . 10.48307 51.41437 45.66501 492 chr4 155859355 155859714 Eya1_peak_2885 449 . 14.43286 50.69167 44.94870 209 chr4 127619949 127620180 Eya1_peak_2772 440 . 19.03096 49.76420 44.03493 98 chr8 9635324 9635499 Eya1_peak_3685 431 . 16.63547 48.88451 43.16126 104 chr10 126681028 126681354 Eya1_peak_410 416 . 19.02312 47.36283 41.66317 194 chr2 172241111 172241320 Eya1_peak_2396 415 . 18.95906 47.25429 41.55551 96 chrX 73869425 73869643 Eya1_peak_4148 404 . 15.98338 46.11438 40.42768 124 chr2 136714189 136714441 Eya1_peak_2295 395 . 18.67864 45.22366 39.55022 118 chr13 100210558 100210856 Eya1_peak_1176 395 . 18.67864 45.22366 39.55022 182 chr8 112128884 112129121 Eya1_peak_3851 390 . 17.90501 44.68640 39.02437 144 chr6 113852455 113852686 Eya1_peak_3335 387 . 16.00205 44.45275 38.79247 95 chr11 115052277 115052540 Eya1_peak_811 386 . 16.80700 44.34334 38.68575 145 chr2 98330084 98330282 Eya1_peak_2236 380 . 17.34015 43.72436 38.07537 136 chr19 10403190 10403441 Eya1_peak_2000 377 . 15.00525 43.38076 37.73551 104 chr14 63713049 63713362 Eya1_peak_1298 377 . 15.00525 43.38076 37.73551 174 chr2 26208194 26208359 Eya1_peak_2102 374 . 15.64662 43.05243 37.42109 94 chr9 99218353 99218632 Eya1_peak_4055 370 . 17.18858 42.70224 37.07518 114 chr7 26489611 26489815 Eya1_peak_3440 370 . 17.60557 42.64975 37.02302 72 chr12 102555085 102555314 Eya1_peak_993 364 . 14.67921 42.02814 36.40963 165 chr7 44770095 44770391 Eya1_peak_3484 362 . 12.72113 41.90360 36.28923 127 chr5 137030208 137030384 Eya1_peak_3133 353 . 14.49327 40.94573 35.34446 89 chr5 121078610 121078834 Eya1_peak_3071 352 . 9.08574 40.83679 35.23641 124 chr4 21712175 21712488 Eya1_peak_2620 351 . 16.92642 40.75261 35.15400 187 chr4 138597875 138598053 Eya1_peak_2833 349 . 16.81469 40.56401 34.97348 114 chr8 19784691 19785123 Eya1_peak_3697 348 . 7.02673 40.44539 34.85579 121 chr7 122670868 122671111 Eya1_peak_3603 347 . 15.39721 40.36196 34.77254 74 chr2 28916126 28916366 Eya1_peak_2115 347 . 15.39721 40.36196 34.77254 105 chr14 37016042 37016212 Eya1_peak_1253 341 . 15.45479 39.72226 34.13923 63 chr15 78119783 78120090 Eya1_peak_1415 338 . 12.23207 39.46757 33.88812 105 chr9 46642808 46642992 Eya1_peak_3940 337 . 16.07206 39.30610 33.73384 90 chr4 140283501 140283714 Eya1_peak_2841 337 . 16.07206 39.30610 33.73384 109 chr9 58060892 58061158 Eya1_peak_3975 328 . 15.95129 38.36762 32.80733 180 chr11 4949326 4949562 Eya1_peak_448 324 . 13.70108 38.02962 32.47639 78 chr17 22230834 22231100 Eya1_peak_1645 320 . 16.34512 37.58119 32.03758 145 chr4 148229755 148229958 Eya1_peak_2852 316 . 10.37253 37.18806 31.64943 95 chr5 120424128 120424289 Eya1_peak_3068 315 . 15.21730 37.12100 31.58309 62 chr8 93469733 93470024 Eya1_peak_3801 311 . 13.37504 36.71734 31.18786 158 chr6 45059214 45059366 Eya1_peak_3226 305 . 15.87841 36.08903 30.57407 82 chr15 26309751 26309933 Eya1_peak_1356 305 . 15.87841 36.08903 30.57407 119 chr6 55108441 55108645 Eya1_peak_3269 303 . 11.25394 35.88099 30.36961 82 chr11 104549983 104550479 Eya1_peak_782 302 . 15.23656 35.72169 30.21530 319 chr4 68955762 68955896 Eya1_peak_2683 300 . 14.29633 35.53844 30.03566 64 chr16 10501954 10502129 Eya1_peak_1509 295 . 14.80396 34.99198 29.50060 61 chr3 87884941 87885569 Eya1_peak_2484 288 . 14.84972 34.36705 28.88548 441 chr6 58330806 58331040 Eya1_peak_3270 287 . 14.35122 34.22439 28.74503 125 chr2 125135862 125136059 Eya1_peak_2277 286 . 13.91018 34.16715 28.68899 87 chr6 30048230 30048518 Eya1_peak_3203 286 . 14.30746 34.14996 28.67266 82 chr4 136907186 136907333 Eya1_peak_2825 285 . 14.22075 34.00229 28.53130 58 chr6 72898765 72899691 Eya1_peak_3284 283 . 14.51866 33.81026 28.34087 775 chr1 25228697 25228890 Eya1_peak_17 282 . 14.89857 33.75362 28.28517 70 chr9 20813141 20813267 Eya1_peak_3901 281 . 12.83324 33.64385 28.17731 66 chr11 83421428 83421554 Eya1_peak_677 275 . 14.07054 33.05334 27.59762 55 chr19 10525247 10525736 Eya1_peak_2001 274 . 14.41325 32.94181 27.48695 268 chr7 30484368 30484466 Eya1_peak_3459 273 . 12.39691 32.84577 27.39436 51 chr17 25400556 25400717 Eya1_peak_1656 273 . 12.39691 32.84577 27.39436 94 chr6 113193842 113194095 Eya1_peak_3329 272 . 14.27376 32.70791 27.26443 70 chr6 8948576 8948727 Eya1_peak_3190 267 . 13.14519 32.15192 26.71788 64 chr18 25500579 25500731 Eya1_peak_1843 266 . 13.52773 32.13007 26.69690 48 chr1 72537068 72537240 Eya1_peak_66 262 . 14.47829 31.69182 26.26226 111 chr14 37068649 37068846 Eya1_peak_1254 262 . 14.47829 31.69182 26.26226 84 chr5 144491402 144491686 Eya1_peak_3163 261 . 12.07087 31.57795 26.15277 84 chr15 101473072 101473202 Eya1_peak_1486 261 . 12.07087 31.57795 26.15277 57 chr3 87993579 87993708 Eya1_peak_2488 261 . 13.97678 31.52990 26.10957 66 chr12 81206308 81206435 Eya1_peak_956 260 . 14.33409 31.45238 26.03709 72 chr5 135806797 135806931 Eya1_peak_3125 258 . 14.23591 31.28930 25.87558 72 chr12 88709454 88709575 Eya1_peak_978 257 . 14.13906 31.12839 25.71800 53 chr9 58841786 58841938 Eya1_peak_3977 254 . 13.99624 30.89097 25.48275 60 chr4 126655447 126655657 Eya1_peak_2766 250 . 13.71907 30.42971 25.02945 59 chr5 115731372 115731591 Eya1_peak_3049 248 . 13.62911 30.27981 24.88590 137 chr9 104569427 104569631 Eya1_peak_4070 248 . 14.01159 30.25391 24.86043 102 chr4 125300595 125300847 Eya1_peak_2758 247 . 10.03128 30.09674 24.71084 137 chr8 22859490 22859713 Eya1_peak_3705 247 . 13.12190 30.09380 24.71033 180 chr5 37243471 37243665 Eya1_peak_2940 242 . 8.80753 29.63080 24.25261 125 chr4 137676185 137676333 Eya1_peak_2828 241 . 12.80853 29.56308 24.18592 72 chr15 84965682 84965843 Eya1_peak_1445 240 . 12.73251 29.43390 24.06037 92 chr11 100758919 100759198 Eya1_peak_759 240 . 13.11315 29.41768 24.04565 109 chr11 75173488 75173618 Eya1_peak_630 240 . 13.49962 29.40532 24.03437 59 chr17 25813614 25813805 Eya1_peak_1657 237 . 12.54635 29.11680 23.74757 94 chr3 89159263 89159459 Eya1_peak_2495 237 . 11.41879 29.07822 23.70951 77 chr15 102470653 102471186 Eya1_peak_1492 237 . 11.41879 29.07822 23.70951 287 chr11 55810855 55811011 Eya1_peak_548 237 . 11.41879 29.07822 23.70951 82 chr14 79769758 79769951 Eya1_peak_1323 236 . 9.78675 28.97095 23.60823 104 chr1 63113477 63114377 Eya1_peak_59 234 . 13.54488 28.83068 23.47242 375 chr10 115184917 115185071 Eya1_peak_387 234 . 13.54488 28.83068 23.47242 84 chr7 28263918 28264083 Eya1_peak_3446 234 . 13.14667 28.81904 23.46490 93 chr2 129715789 129715958 Eya1_peak_2288 234 . 12.75112 28.80957 23.45582 92 chr5 134638803 134639293 Eya1_peak_3119 233 . 12.71212 28.74388 23.39314 424 chr2 79454293 79454427 Eya1_peak_2207 233 . 12.71212 28.74388 23.39314 67 chr9 64666646 64666840 Eya1_peak_4001 233 . 13.06130 28.67699 23.32736 123 chr10 60445228 60445536 Eya1_peak_279 230 . 10.39995 28.40549 23.05923 166 chr10 127256182 127256343 Eya1_peak_417 229 . 12.85264 28.32931 22.98425 87 chr8 20296773 20297361 Eya1_peak_3701 227 . 7.43917 28.14086 22.79840 290 chr18 42396150 42396368 Eya1_peak_1883 227 . 12.69046 28.05851 22.71919 122 chr2 25318878 25319146 Eya1_peak_2095 226 . 12.65055 27.99180 22.65529 141 chr2 180104445 180104659 Eya1_peak_2413 225 . 11.09274 27.84700 22.51441 136 chr15 80277767 80277892 Eya1_peak_1428 223 . 12.83461 27.65584 22.33058 70 chr17 72603209 72603409 Eya1_peak_1785 223 . 11.69167 27.64426 22.31924 95 chr5 36836090 36836213 Eya1_peak_2935 221 . 11.97941 27.50118 22.17908 66 chr1 38939741 38939850 Eya1_peak_30 221 . 12.70877 27.44721 22.12621 49 chr19 35833124 35833289 Eya1_peak_2021 221 . 13.07818 27.42266 22.10222 69 chr1 70725721 70725836 Eya1_peak_65 221 . 13.07818 27.42266 22.10222 58 chr16 17201070 17201443 Eya1_peak_1523 221 . 13.07818 27.42266 22.10222 160 chr12 112141406 112141544 Eya1_peak_1014 221 . 13.07818 27.42266 22.10222 82 chr2 178277338 178277447 Eya1_peak_2404 220 . 12.66737 27.37853 22.06355 54 chr13 25269142 25269418 Eya1_peak_1064 220 . 12.66737 27.37853 22.06355 100 chr17 87798525 87798678 Eya1_peak_1811 214 . 11.93728 26.79274 21.48707 61 chr5 27737222 27737424 Eya1_peak_2905 214 . 9.29768 26.75250 21.44795 114 chr7 121596533 121596651 Eya1_peak_3600 214 . 12.26775 26.71403 21.41153 64 chr2 70559664 70559781 Eya1_peak_2186 214 . 12.26775 26.71403 21.41153 41 chr8 124793291 124793482 Eya1_peak_3879 213 . 12.60031 26.63480 21.33681 130 chr9 56738429 56738534 Eya1_peak_3961 213 . 10.76670 26.62870 21.33154 38 chr2 29573696 29573853 Eya1_peak_2117 213 . 10.76670 26.62870 21.33154 85 chr7 25146039 25146178 Eya1_peak_3432 211 . 12.11488 26.45898 21.16973 65 chr6 113881919 113882081 Eya1_peak_3336 210 . 11.32656 26.37718 21.08873 127 chr4 125590607 125590770 Eya1_peak_2761 210 . 12.39238 26.29144 21.00438 63 chr11 35798959 35799121 Eya1_peak_502 210 . 12.39238 26.29144 21.00438 110 chr4 155397640 155397757 Eya1_peak_2881 208 . 11.89258 26.08712 20.80503 54 chr3 91213400 91213576 Eya1_peak_2505 207 . 12.61147 26.03038 20.74978 55 chr1 8123236 8123343 Eya1_peak_5 207 . 12.61147 26.03038 20.74978 55 chr16 7740516 7740654 Eya1_peak_1502 207 . 12.61147 26.03038 20.74978 70 chr1 75263096 75263292 Eya1_peak_74 204 . 12.07359 25.76395 20.49252 48 chr1 127496887 127497019 Eya1_peak_116 204 . 11.67829 25.72738 20.45681 69 chr8 20424068 20424639 Eya1_peak_3702 203 . 5.21851 25.62575 20.35870 379 chr2 179193798 179193992 Eya1_peak_2408 202 . 8.02502 25.52196 20.25605 106 chr9 108190094 108190226 Eya1_peak_4087 202 . 11.53967 25.49394 20.22894 64 chr14 32597330 32597466 Eya1_peak_1243 202 . 11.53967 25.49394 20.22894 69 chr2 77945609 77946094 Eya1_peak_2205 201 . 8.00102 25.46328 20.19978 414 chr7 79499292 79499495 Eya1_peak_3520 201 . 10.44066 25.42371 20.16041 140 chr15 84086472 84086599 Eya1_peak_1440 201 . 10.44066 25.42371 20.16041 58 chr9 57606124 57606281 Eya1_peak_3969 199 . 12.11002 25.20601 19.95392 96 chr17 27466780 27466908 Eya1_peak_1664 198 . 11.69745 25.13922 19.88793 64 chr19 53390108 53390437 Eya1_peak_2055 198 . 10.96145 25.12429 19.87337 258 chr4 125835363 125835501 Eya1_peak_2762 196 . 11.95014 24.94278 19.69465 66 chr1 39900911 39901328 Eya1_peak_35 196 . 11.95014 24.94278 19.69465 356 chr14 80215912 80216097 Eya1_peak_1326 195 . 11.48281 24.78126 19.53751 123 chr12 51829066 51829562 Eya1_peak_898 195 . 11.48281 24.78126 19.53751 443 chr7 110701763 110701977 Eya1_peak_3573 194 . 11.79444 24.68611 19.44514 150 chr8 84454688 84454862 Eya1_peak_3773 194 . 12.14477 24.65444 19.41604 55 chrX 15963125 15963239 Eya1_peak_4147 193 . 8.80862 24.58018 19.34808 69 chr2 156652957 156653099 Eya1_peak_2337 193 . 8.80862 24.58018 19.34808 69 chr7 18951534 18951660 Eya1_peak_3420 192 . 11.64273 24.43570 19.20666 54 chr15 79791635 79791834 Eya1_peak_1422 192 . 11.27590 24.43500 19.20636 85 chr5 137031177 137031280 Eya1_peak_3135 191 . 10.89316 24.39605 19.16798 49 chr3 114904085 114904296 Eya1_peak_2550 190 . 10.11461 24.23245 19.00677 139 chr1 146106902 146107194 Eya1_peak_149 190 . 10.11461 24.23245 19.00677 151 chr11 33680216 33680365 Eya1_peak_498 190 . 10.11461 24.23245 19.00677 65 chr10 81037459 81037598 Eya1_peak_339 190 . 10.11461 24.23245 19.00677 70 chr6 86525398 86526161 Eya1_peak_3305 189 . 11.49488 24.19125 18.97339 559 chr11 101602624 101602774 Eya1_peak_761 189 . 11.49488 24.19125 18.97339 61 chr4 103572053 103572216 Eya1_peak_2714 188 . 11.42235 24.07118 18.85390 101 chr8 20550250 20550675 Eya1_peak_3703 186 . 7.00446 23.88376 18.67354 235 chr8 84687230 84687871 Eya1_peak_3776 185 . 11.58438 23.73598 18.52746 380 chr6 95223626 95223782 Eya1_peak_3322 185 . 11.58438 23.73598 18.52746 51 chr5 52189936 52190422 Eya1_peak_2949 185 . 11.58438 23.73598 18.52746 282 chr3 89764407 89764587 Eya1_peak_2498 184 . 10.82095 23.66871 18.46150 60 chr2 155775683 155775849 Eya1_peak_2331 184 . 11.17557 23.66171 18.45594 107 chr1 74891632 74891795 Eya1_peak_72 184 . 11.50791 23.61046 18.40484 91 chr7 138084022 138084287 Eya1_peak_3664 183 . 8.56409 23.51211 18.30942 143 chr11 51606042 51606778 Eya1_peak_526 182 . 11.07303 23.49114 18.29048 346 chr19 47006443 47006633 Eya1_peak_2049 182 . 11.43245 23.48652 18.28747 83 chr13 9763667 9764552 Eya1_peak_1030 182 . 11.39508 23.42512 18.22775 568 chr7 122969970 122970710 Eya1_peak_3604 181 . 11.35797 23.36411 18.16800 183 chr3 19694584 19694718 Eya1_peak_2438 181 . 11.35797 23.36411 18.16800 60 chrX 147639717 147639944 Eya1_peak_4157 181 . 11.67806 23.29548 18.10246 77 chr5 116914996 116915148 Eya1_peak_3059 181 . 11.67806 23.29548 18.10246 79 chr4 12171396 12171804 Eya1_peak_2614 181 . 11.67806 23.29548 18.10246 135 chr18 76847502 76847618 Eya1_peak_1924 181 . 11.67806 23.29548 18.10246 51 chr10 41071875 41071989 Eya1_peak_259 181 . 11.67806 23.29548 18.10246 50 chr2 143546889 143547023 Eya1_peak_2298 179 . 11.24805 23.18331 17.99706 70 chr11 74619244 74619433 Eya1_peak_619 179 . 11.60176 23.17092 17.98487 107 chr15 78066632 78066758 Eya1_peak_1414 179 . 11.21188 23.12377 17.93847 77 chr9 43959624 43959808 Eya1_peak_3926 178 . 9.78857 23.05537 17.87166 93 chr8 84471316 84471557 Eya1_peak_3774 178 . 9.78857 23.05537 17.87166 160 chr8 123041391 123042236 Eya1_peak_3872 178 . 10.80859 23.04981 17.87166 435 chr5 141985168 141985312 Eya1_peak_3152 178 . 9.78857 23.05537 17.87166 70 chr4 140439952 140440172 Eya1_peak_2843 178 . 9.78857 23.05537 17.87166 138 chr2 21367380 21367566 Eya1_peak_2087 178 . 9.78857 23.05537 17.87166 81 chr2 180756015 180756195 Eya1_peak_2419 178 . 9.78857 23.05537 17.87166 88 chr17 73488011 73488159 Eya1_peak_1788 178 . 9.78857 23.05537 17.87166 82 chr15 89453390 89453557 Eya1_peak_1457 178 . 6.85054 22.98327 17.80807 118 chr12 105322217 105322521 Eya1_peak_998 177 . 11.10475 22.94730 17.77261 233 chr14 27596431 27596562 Eya1_peak_1227 177 . 10.74444 22.94242 17.76820 47 chr11 99229979 99230488 Eya1_peak_753 177 . 10.74444 22.94242 17.76820 310 chr4 44511811 44511959 Eya1_peak_2651 177 . 11.44337 22.91233 17.73956 76 chr1 37218519 37218691 Eya1_peak_26 177 . 11.44337 22.91233 17.73956 62 chr18 7869685 7870098 Eya1_peak_1826 176 . 11.40444 22.84877 17.67680 345 chr9 106656272 106656432 Eya1_peak_4077 176 . 10.99965 22.77395 17.60241 49 chr6 87850370 87850956 Eya1_peak_3308 176 . 10.99965 22.77395 17.60241 119 chr2 156179609 156180148 Eya1_peak_2334 176 . 10.99965 22.77395 17.60241 371 chr4 136601978 136602323 Eya1_peak_2823 174 . 11.28924 22.66059 17.49288 249 chr4 129120917 129121245 Eya1_peak_2779 174 . 11.28924 22.66059 17.49288 148 chr14 49172427 49172680 Eya1_peak_1265 174 . 11.28924 22.66059 17.49288 183 chr1 134664961 134665103 Eya1_peak_136 174 . 11.28924 22.66059 17.49288 46 chr18 38075457 38075672 Eya1_peak_1875 173 . 11.21372 22.53719 17.37366 69 chr7 4178527 4178727 Eya1_peak_3395 172 . 8.31956 22.45657 17.29459 85 chr4 9269493 9269622 Eya1_peak_2608 172 . 8.31956 22.45657 17.29459 64 chr8 74993632 74994201 Eya1_peak_3758 172 . 10.79532 22.43619 17.27610 287 chr11 102393330 102393560 Eya1_peak_768 171 . 10.72888 22.32615 17.16902 157 chr4 132211312 132212032 Eya1_peak_2797 171 . 10.69597 22.27159 17.11521 567 chr9 97110678 97111065 Eya1_peak_4052 170 . 10.66326 22.21734 17.06153 153 chr8 110196824 110196940 Eya1_peak_3844 170 . 10.66326 22.21734 17.06153 64 chr11 6016490 6016608 Eya1_peak_456 170 . 10.66326 22.21734 17.06153 49 chr9 59578343 59578528 Eya1_peak_3984 169 . 10.92150 22.05908 16.90788 94 chr5 111901765 111901956 Eya1_peak_3027 169 . 10.92150 22.05908 16.90788 132 chr3 82412562 82412651 Eya1_peak_2482 169 . 10.92150 22.05908 16.90788 45 chr9 27308178 27308324 Eya1_peak_3913 168 . 11.21136 21.95418 16.80686 65 chr8 111941263 111941458 Eya1_peak_3850 168 . 10.50266 21.95053 16.80686 124 chr18 66561051 66561213 Eya1_peak_1911 168 . 11.21136 21.95418 16.80686 113 chr11 56812248 56812393 Eya1_peak_550 168 . 11.21136 21.95418 16.80686 97 chr8 121736355 121736468 Eya1_peak_3866 167 . 10.14249 21.92714 16.78704 50 chr5 146644638 146644821 Eya1_peak_3169 167 . 11.17678 21.89794 16.75844 111 chr7 16147765 16147930 Eya1_peak_3410 167 . 9.46253 21.89293 16.75402 76 chr7 131960671 131960827 Eya1_peak_3652 167 . 9.46253 21.89293 16.75402 70 chr4 124317179 124317369 Eya1_peak_2754 167 . 9.46253 21.89293 16.75402 95 chr17 27228668 27228818 Eya1_peak_1663 167 . 9.46253 21.89293 16.75402 72 chr16 35302506 35303112 Eya1_peak_1564 167 . 9.46253 21.89293 16.75402 40 chr11 98314191 98314325 Eya1_peak_744 167 . 9.46253 21.89293 16.75402 69 chr10 79718075 79718250 Eya1_peak_315 167 . 9.46253 21.89293 16.75402 63 chr10 29146977 29147095 Eya1_peak_243 167 . 9.46253 21.89293 16.75402 56 chr11 82514890 82515002 Eya1_peak_675 165 . 10.34683 21.69085 16.56532 51 chr8 71483976 71484105 Eya1_peak_3751 163 . 10.57695 21.49368 16.37304 47 chr14 121378690 121379149 Eya1_peak_1343 163 . 10.57695 21.49368 16.37304 281 chr4 152287046 152287180 Eya1_peak_2869 163 . 10.22545 21.48801 16.36997 67 chr9 66307432 66307657 Eya1_peak_4009 162 . 8.07502 21.41391 16.29678 96 chr10 112928514 112928962 Eya1_peak_386 162 . 8.07502 21.41391 16.29678 242 chr4 81442452 81442762 Eya1_peak_2688 162 . 10.83807 21.34694 16.23245 270 chr18 77417640 77417764 Eya1_peak_1928 162 . 10.83807 21.34694 16.23245 53 chr1 192472442 192472628 Eya1_peak_215 162 . 10.83807 21.34694 16.23245 133 chr11 59584686 59584797 Eya1_peak_561 162 . 10.83807 21.34694 16.23245 47 chr2 180417826 180417975 Eya1_peak_2415 161 . 10.10689 21.28935 16.17681 97 chr13 99900547 99900724 Eya1_peak_1175 161 . 10.80170 21.28774 16.17522 78 chr7 90442829 90443670 Eya1_peak_3542 161 . 10.76558 21.22892 16.11720 179 chr4 131658046 131658174 Eya1_peak_2794 160 . 10.72969 21.17048 16.06041 57 chr18 63977172 63977328 Eya1_peak_1906 160 . 10.72969 21.17048 16.06041 67 chr17 74528981 74529113 Eya1_peak_1793 160 . 10.72969 21.17048 16.06041 62 chr9 110532687 110533379 Eya1_peak_4104 160 . 10.34843 21.11728 16.00886 251 chr12 86213191 86213346 Eya1_peak_970 160 . 10.69404 21.11242 16.00449 67 chr7 129469619 129469785 Eya1_peak_3646 158 . 10.62345 20.99741 15.89252 66 chr8 9769203 9769332 Eya1_peak_3686 158 . 10.25349 20.96051 15.85626 31 chr8 95331431 95331779 Eya1_peak_3812 158 . 10.25349 20.96051 15.85626 278 chr5 116714391 116714511 Eya1_peak_3057 158 . 10.25349 20.96051 15.85626 70 chr4 136311048 136311558 Eya1_peak_2821 158 . 10.25349 20.96051 15.85626 84 chr19 41661111 41661246 Eya1_peak_2030 156 . 10.12957 20.75550 15.65942 63 chr11 60105176 60106260 Eya1_peak_563 156 . 10.12957 20.75550 15.65942 191 chr4 153679297 153679421 Eya1_peak_2875 156 . 9.13649 20.74566 15.64987 60 chr4 127021372 127022284 Eya1_peak_2770 156 . 9.13649 20.74566 15.64987 368 chr2 167188823 167189204 Eya1_peak_2386 156 . 9.13649 20.74566 15.64987 260 chr19 6502708 6502895 Eya1_peak_1977 156 . 9.13649 20.74566 15.64987 67 chr19 47016608 47016760 Eya1_peak_2050 156 . 9.13649 20.74566 15.64987 51 chr17 91092801 91092976 Eya1_peak_1816 156 . 9.13649 20.74566 15.64987 105 chr12 108994780 108994927 Eya1_peak_1006 156 . 9.13649 20.74566 15.64987 75 chr12 106115158 106115318 Eya1_peak_1000 156 . 9.13649 20.74566 15.64987 70 chr12 102550607 102550779 Eya1_peak_992 156 . 9.13649 20.74566 15.64987 94 chr11 83417206 83417312 Eya1_peak_676 156 . 9.13649 20.74566 15.64987 55 chr1 152956322 152956491 Eya1_peak_155 156 . 9.13649 20.74566 15.64987 89 chr5 135843519 135843678 Eya1_peak_3126 156 . 10.45098 20.71614 15.63094 90 chr5 113407464 113407592 Eya1_peak_3035 156 . 10.45098 20.71614 15.63094 70 chr4 153357659 153357770 Eya1_peak_2874 156 . 9.76715 20.71686 15.63094 52 chr9 54271039 54271153 Eya1_peak_3955 155 . 10.74465 20.63129 15.54729 29 chr7 59228997 59229530 Eya1_peak_3503 155 . 10.74465 20.63129 15.54729 201 chr5 63689227 63689318 Eya1_peak_2955 155 . 10.74465 20.63129 15.54729 54 chr2 154076391 154076499 Eya1_peak_2317 155 . 10.74465 20.63129 15.54729 51 chr16 33251451 33251775 Eya1_peak_1560 154 . 9.35622 20.57506 15.49982 72 chr2 80580522 80581095 Eya1_peak_2209 154 . 10.35017 20.55151 15.47678 387 chr7 123235571 123235699 Eya1_peak_3607 154 . 10.67445 20.51757 15.44345 70 chr11 105182016 105182537 Eya1_peak_784 154 . 9.00442 20.50887 15.43542 292 chr6 92091693 92092047 Eya1_peak_3319 154 . 10.31699 20.49730 15.42400 75 chr12 3806298 3806724 Eya1_peak_856 154 . 10.31699 20.49730 15.42400 295 chr2 26205178 26205345 Eya1_peak_2101 153 . 9.94922 20.45624 15.38370 131 chr2 119477302 119477631 Eya1_peak_2266 153 . 9.94922 20.45624 15.38370 48 chr12 3955550 3955646 Eya1_peak_861 153 . 9.94922 20.45624 15.38370 61 chr7 24727773 24727900 Eya1_peak_3428 153 . 10.28403 20.44342 15.37248 62 chr2 172320988 172321167 Eya1_peak_2397 153 . 10.25128 20.38986 15.31972 112 chr4 141139345 141139666 Eya1_peak_2846 152 . 10.21873 20.33661 15.26927 242 chr2 163889528 163889648 Eya1_peak_2368 151 . 10.15425 20.23107 15.16580 62 chr12 80435129 80435444 Eya1_peak_948 151 . 10.15425 20.23107 15.16580 168 chr2 157663726 157663873 Eya1_peak_2348 149 . 10.38691 20.05170 14.99107 82 chr15 8443802 8444267 Eya1_peak_1346 149 . 10.38691 20.05170 14.99107 233 chr2 91921278 91921406 Eya1_peak_2222 149 . 9.69041 20.02477 14.96701 67 chr2 154436633 154436974 Eya1_peak_2318 149 . 10.02772 20.02365 14.96592 59 chr7 44335740 44335866 Eya1_peak_3482 149 . 10.35205 19.99519 14.93797 61 chr15 73026826 73027022 Eya1_peak_1393 149 . 10.35205 19.99519 14.93797 107 chr1 167079655 167079740 Eya1_peak_181 148 . 9.96562 19.92173 14.86680 35 chr11 118685587 118685695 Eya1_peak_835 148 . 10.28304 19.88329 14.82890 55 chr9 63151246 63151354 Eya1_peak_3993 147 . 9.24898 19.83296 14.78078 52 chr4 151186524 151186729 Eya1_peak_2861 147 . 9.24898 19.83296 14.78078 97 chr8 126404662 126404774 Eya1_peak_3882 147 . 10.24887 19.82787 14.77639 56 chr3 90508983 90509410 Eya1_peak_2504 147 . 10.21493 19.77282 14.72249 221 chr10 80399072 80399394 Eya1_peak_330 147 . 10.21493 19.77282 14.72249 104 chr5 143527509 143527983 Eya1_peak_3161 146 . 9.84371 19.72131 14.67198 301 chr4 58911660 58911939 Eya1_peak_2671 146 . 10.18122 19.71811 14.67198 154 chr11 81005975 81006074 Eya1_peak_669 146 . 9.84371 19.72131 14.67198 64 chr18 36004725 36004901 Eya1_peak_1872 146 . 10.14773 19.66375 14.61959 91 chr8 4324606 4325023 Eya1_peak_3681 145 . 8.81044 19.61410 14.57058 246 chr5 148071930 148072110 Eya1_peak_3176 145 . 8.81044 19.61410 14.57058 74 chr4 140358224 140358382 Eya1_peak_2842 145 . 8.81044 19.61410 14.57058 57 chr3 31309004 31309146 Eya1_peak_2445 145 . 8.81044 19.61410 14.57058 72 chr3 118431459 118431649 Eya1_peak_2554 145 . 8.81044 19.61410 14.57058 128 chr2 94245478 94245636 Eya1_peak_2233 145 . 10.11445 19.60974 14.57058 86 chr2 158584723 158584892 Eya1_peak_2354 145 . 8.81044 19.61410 14.57058 68 chr17 83010982 83011137 Eya1_peak_1801 145 . 8.81044 19.61410 14.57058 80 chr17 39107409 39107510 Eya1_peak_1720 145 . 8.81044 19.61410 14.57058 40 chr12 86983589 86983730 Eya1_peak_973 145 . 8.81044 19.61410 14.57058 45 chr10 89224654 89224792 Eya1_peak_361 145 . 8.81044 19.61410 14.57058 67 chr4 128042767 128042895 Eya1_peak_2774 144 . 9.39182 19.52353 14.49168 58 chr4 126202274 126202650 Eya1_peak_2763 144 . 9.39182 19.52353 14.49168 303 chr10 60914531 60914664 Eya1_peak_280 144 . 9.39182 19.52353 14.49168 56 chr15 27655140 27655234 Eya1_peak_1357 144 . 10.04856 19.50272 14.47203 55 chr12 83632295 83632904 Eya1_peak_961 144 . 10.04856 19.50272 14.47203 142 chr1 86527785 86528001 Eya1_peak_93 144 . 9.69546 19.47700 14.44978 146 chr1 74391728 74391961 Eya1_peak_68 144 . 9.69546 19.47700 14.44978 188 chr3 105275375 105275513 Eya1_peak_2540 144 . 10.01593 19.44970 14.42279 65 chr2 164968564 164968847 Eya1_peak_2375 143 . 7.58596 19.36886 14.34354 100 chr17 6321824 6322006 Eya1_peak_1629 143 . 7.58596 19.36886 14.34354 106 chr11 105181635 105181943 Eya1_peak_783 143 . 7.58596 19.36886 14.34354 206 chr6 35539670 35539817 Eya1_peak_3216 143 . 10.27795 19.32762 14.30448 61 chr12 18467145 18467323 Eya1_peak_875 143 . 10.27795 19.32762 14.30448 48 chr10 7589682 7589929 Eya1_peak_224 143 . 10.27795 19.32762 14.30448 122 chr2 179200643 179200756 Eya1_peak_2409 142 . 9.91931 19.29261 14.27566 41 chr12 112673599 112673946 Eya1_peak_1016 142 . 9.91931 19.29261 14.27566 260 chr17 80061466 80062025 Eya1_peak_1796 142 . 9.88752 19.24088 14.22487 147 chr13 99564493 99564605 Eya1_peak_1174 142 . 9.88752 19.24088 14.22487 39 chr7 123123957 123124161 Eya1_peak_3605 142 . 9.55160 19.23926 14.22408 155 chr18 25752876 25753035 Eya1_peak_1846 142 . 9.55160 19.23926 14.22408 59 chr2 157970788 157970940 Eya1_peak_2350 141 . 9.49525 19.14593 14.13433 62 chr9 64624676 64624805 Eya1_peak_4000 141 . 9.82454 19.13836 14.12684 60 chr4 129514113 129514463 Eya1_peak_2783 141 . 9.82454 19.13836 14.12684 95 chr8 86425516 86425640 Eya1_peak_3788 139 . 9.73155 18.98685 13.97791 83 chr18 77274357 77274452 Eya1_peak_1927 139 . 9.73155 18.98685 13.97791 49 chr15 86932807 86932930 Eya1_peak_1449 139 . 9.73155 18.98685 13.97791 51 chr8 123414387 123414507 Eya1_peak_3874 137 . 9.61028 18.78895 13.78484 71 chr9 57764834 57765104 Eya1_peak_3973 137 . 9.27633 18.78221 13.77869 114 chr4 32601239 32601381 Eya1_peak_2624 137 . 9.27633 18.78221 13.77869 90 chr4 148293339 148293553 Eya1_peak_2854 137 . 9.27633 18.78221 13.77869 132 chr2 174330206 174330835 Eya1_peak_2402 137 . 9.27633 18.78221 13.77869 573 chr14 46788088 46788265 Eya1_peak_1260 137 . 9.27633 18.78221 13.77869 98 chr7 124199057 124199195 Eya1_peak_3609 137 . 9.93574 18.77567 13.77311 72 chr4 136144090 136144289 Eya1_peak_2819 137 . 9.24967 18.73779 13.73852 39 chr8 119258689 119258895 Eya1_peak_3859 136 . 9.83638 18.61530 13.61923 93 chr16 91647901 91648371 Eya1_peak_1601 136 . 9.83638 18.61530 13.61923 175 chr2 92401271 92401451 Eya1_peak_2226 135 . 9.80370 18.56254 13.56738 118 chr11 72607632 72607775 Eya1_peak_615 135 . 9.80370 18.56254 13.56738 95 chr5 121712411 121712827 Eya1_peak_3075 135 . 9.77123 18.51012 13.51636 357 chr7 7080954 7081184 Eya1_peak_3402 135 . 8.48440 18.49883 13.50733 54 chr7 33836732 33836956 Eya1_peak_3467 135 . 8.48440 18.49883 13.50733 107 chr7 144294418 144294512 Eya1_peak_3675 135 . 8.48440 18.49883 13.50733 46 chr7 118001237 118001389 Eya1_peak_3588 135 . 8.48440 18.49883 13.50733 65 chr6 89242479 89242586 Eya1_peak_3315 135 . 8.48440 18.49883 13.50733 64 chr4 153189629 153189775 Eya1_peak_2873 135 . 8.48440 18.49883 13.50733 95 chr4 139059694 139059859 Eya1_peak_2834 135 . 8.48440 18.49883 13.50733 100 chr2 25608099 25608412 Eya1_peak_2099 135 . 9.43394 18.50051 13.50733 123 chr18 64042669 64042829 Eya1_peak_1907 135 . 8.48440 18.49883 13.50733 67 chr17 46856876 46857518 Eya1_peak_1749 135 . 8.48440 18.49883 13.50733 226 chr1 178336968 178337653 Eya1_peak_197 135 . 9.43394 18.50051 13.50733 344 chr11 52099015 52099210 Eya1_peak_530 135 . 9.43394 18.50051 13.50733 58 chr9 113707834 113708186 Eya1_peak_4110 134 . 9.73899 18.45803 13.47895 210 chr7 81493354 81493552 Eya1_peak_3534 134 . 9.73899 18.45803 13.47895 137 chr18 77774149 77774437 Eya1_peak_1929 134 . 9.40518 18.45338 13.47508 88 chr8 10255830 10256031 Eya1_peak_3687 133 . 7.34143 18.36732 13.39028 87 chr6 127767904 127768115 Eya1_peak_3373 133 . 7.34143 18.36732 13.39028 54 chr2 93071776 93071900 Eya1_peak_2230 133 . 7.34143 18.36732 13.39028 72 chr2 31346212 31346375 Eya1_peak_2126 133 . 7.34143 18.36732 13.39028 62 chr8 13106013 13106320 Eya1_peak_3694 133 . 9.67512 18.35484 13.38054 145 chr9 45984334 45984800 Eya1_peak_3938 133 . 9.01648 18.34783 13.37449 112 chr9 105693984 105694064 Eya1_peak_4073 133 . 9.01648 18.34783 13.37449 41 chr5 137553469 137553764 Eya1_peak_3141 133 . 9.01648 18.34783 13.37449 97 chr16 33380972 33381467 Eya1_peak_1561 133 . 9.64350 18.30373 13.33243 194 chr1 133025109 133025353 Eya1_peak_126 133 . 8.66374 18.28217 13.31144 66 chr9 100023787 100023888 Eya1_peak_4057 132 . 9.61209 18.25295 13.28294 40 chr6 89070121 89070258 Eya1_peak_3314 132 . 9.61209 18.25295 13.28294 46 chr16 34400465 34400607 Eya1_peak_1563 131 . 9.51906 18.10246 13.13620 48 chr4 124882440 124882530 Eya1_peak_2757 130 . 9.48845 18.05291 13.08723 43 chr7 57592312 57592438 Eya1_peak_3502 130 . 9.15399 18.04067 13.07905 61 chr6 35539348 35539619 Eya1_peak_3215 130 . 9.81124 18.04406 13.07905 199 chr4 89313629 89313752 Eya1_peak_2695 130 . 9.81124 18.04406 13.07905 66 chr4 8536050 8536394 Eya1_peak_2607 130 . 9.15399 18.04067 13.07905 127 chr3 152821318 152821453 Eya1_peak_2593 130 . 9.15399 18.04067 13.07905 70 chr2 146226685 146226805 Eya1_peak_2301 130 . 9.81124 18.04406 13.07905 71 chr18 88893584 88894071 Eya1_peak_1944 130 . 9.81124 18.04406 13.07905 408 chr17 28575544 28575734 Eya1_peak_1670 130 . 9.15399 18.04067 13.07905 123 chr15 72201011 72201104 Eya1_peak_1390 130 . 9.81124 18.04406 13.07905 48 chr10 128377139 128377627 Eya1_peak_423 130 . 9.15399 18.04067 13.07905 72 chr4 42999728 43000327 Eya1_peak_2644 130 . 9.45804 18.00367 13.04851 361 chr4 148286816 148286918 Eya1_peak_2853 130 . 7.92306 18.00067 13.04664 69 chr3 145118654 145118769 Eya1_peak_2583 130 . 9.78098 17.99549 13.04153 63 chr1 131097106 131097475 Eya1_peak_119 130 . 9.78098 17.99549 13.04153 327 chr11 71937240 71937369 Eya1_peak_608 129 . 9.71352 17.88723 12.93657 62 chr11 49203617 49203769 Eya1_peak_515 129 . 9.71352 17.88723 12.93657 65 chr7 131917500 131917602 Eya1_peak_3651 128 . 9.68014 17.83365 12.88478 60 chr14 16365376 16365978 Eya1_peak_1207 128 . 9.68014 17.83365 12.88478 293 chr8 126592834 126593367 Eya1_peak_3885 128 . 9.02015 17.81987 12.87121 127 chr5 37009889 37010211 Eya1_peak_2937 128 . 9.33831 17.80962 12.86110 250 chr9 75683880 75684027 Eya1_peak_4029 128 . 9.30885 17.76183 12.81403 66 chr9 109875974 109876392 Eya1_peak_4101 128 . 9.30885 17.76183 12.81403 115 chr16 94570578 94570722 Eya1_peak_1605 128 . 9.30885 17.76183 12.81403 54 chr12 69892697 69892904 Eya1_peak_927 128 . 9.30885 17.76183 12.81403 129 chr2 4881788 4882270 Eya1_peak_2074 127 . 9.61406 17.72760 12.78270 228 chr4 124633416 124633556 Eya1_peak_2755 127 . 9.27958 17.71432 12.76956 65 chr2 172042193 172042371 Eya1_peak_2394 127 . 9.27958 17.71432 12.76956 82 chr12 31949827 31949943 Eya1_peak_889 127 . 9.58136 17.67511 12.73094 50 chr1 160906443 160907077 Eya1_peak_170 127 . 9.58136 17.67511 12.73094 207 chr6 117906848 117907607 Eya1_peak_3349 126 . 9.54888 17.62297 12.67982 248 chr12 113188123 113188230 Eya1_peak_1022 126 . 9.54888 17.62297 12.67982 57 chr8 119164207 119164292 Eya1_peak_3858 126 . 8.89018 17.60475 12.66231 45 chr7 45873277 45873604 Eya1_peak_3494 126 . 8.89018 17.60475 12.66231 262 chr6 47767735 47767890 Eya1_peak_3242 126 . 5.18064 17.60359 12.66231 96 chr5 121068818 121068935 Eya1_peak_3070 126 . 8.89018 17.60475 12.66231 77 chr11 104198019 104198141 Eya1_peak_779 126 . 8.89018 17.60475 12.66231 50 chr4 148626368 148626726 Eya1_peak_2857 126 . 7.97906 17.59257 12.65156 216 chr16 97851265 97851506 Eya1_peak_1615 126 . 9.19285 17.57345 12.63265 82 chr8 20122285 20123015 Eya1_peak_3700 126 . 3.50182 17.57015 12.63046 460 chr8 40511786 40512130 Eya1_peak_3722 125 . 9.48458 17.51974 12.58116 179 chr5 99707418 99707500 Eya1_peak_3000 125 . 9.48458 17.51974 12.58116 55 chr17 69439314 69439460 Eya1_peak_1781 125 . 9.48458 17.51974 12.58116 95 chr4 120866402 120866559 Eya1_peak_2745 125 . 9.13593 17.48089 12.54435 98 chr4 121214830 121215002 Eya1_peak_2747 124 . 9.42113 17.41786 12.48246 63 chr18 38217110 38217214 Eya1_peak_1876 124 . 9.42113 17.41786 12.48246 61 chr9 78481046 78481605 Eya1_peak_4030 124 . 8.15836 17.40049 12.46604 253 chr9 49341152 49341294 Eya1_peak_3947 124 . 8.15836 17.40049 12.46604 66 chr7 84085100 84085250 Eya1_peak_3537 124 . 8.15836 17.40049 12.46604 85 chr6 113077450 113078166 Eya1_peak_3328 124 . 8.15836 17.40049 12.46604 243 chr4 155491449 155492265 Eya1_peak_2882 124 . 8.15836 17.40049 12.46604 418 chr3 88220950 88221124 Eya1_peak_2489 124 . 8.15836 17.40049 12.46604 99 chr2 25500896 25501251 Eya1_peak_2097 124 . 8.15836 17.40049 12.46604 133 chr2 152081901 152082036 Eya1_peak_2303 124 . 8.15836 17.40049 12.46604 71 chr2 132781744 132781971 Eya1_peak_2294 124 . 8.15836 17.40049 12.46604 54 chr2 104816345 104816786 Eya1_peak_2247 124 . 8.15836 17.40049 12.46604 241 chr18 70411115 70411244 Eya1_peak_1912 124 . 8.15836 17.40049 12.46604 61 chr17 84820739 84820865 Eya1_peak_1807 124 . 8.15836 17.40049 12.46604 66 chr15 88733720 88733929 Eya1_peak_1454 124 . 8.15836 17.40049 12.46604 59 chr14 29657148 29657299 Eya1_peak_1228 124 . 8.15836 17.40049 12.46604 70 chr10 71403717 71403833 Eya1_peak_300 124 . 8.15836 17.40049 12.46604 60 chr10 4387214 4387543 Eya1_peak_219 124 . 8.15836 17.40049 12.46604 102 chr10 128059307 128059675 Eya1_peak_418 124 . 8.15836 17.40049 12.46604 243 chr10 110676637 110676790 Eya1_peak_382 124 . 8.15836 17.40049 12.46604 62 chr8 105693810 105693911 Eya1_peak_3829 124 . 7.09690 17.38039 12.45766 38 chr6 113282089 113282216 Eya1_peak_3330 124 . 7.09690 17.38039 12.45766 58 chr4 46992961 46993103 Eya1_peak_2658 124 . 7.09690 17.38039 12.45766 70 chr2 156677010 156677161 Eya1_peak_2338 124 . 7.09690 17.38039 12.45766 93 chr1 90028488 90028604 Eya1_peak_99 124 . 7.09690 17.38039 12.45766 62 chr13 23990956 23991111 Eya1_peak_1059 124 . 7.09690 17.38039 12.45766 85 chr11 82371712 82371850 Eya1_peak_674 124 . 7.09690 17.38039 12.45766 67 chr7 80993064 80993518 Eya1_peak_3532 124 . 9.05185 17.34402 12.42535 294 chr10 90827073 90827171 Eya1_peak_365 123 . 9.35853 17.31731 12.39896 49 chr9 40269711 40269789 Eya1_peak_3920 123 . 9.02417 17.29891 12.38175 38 chr4 63544858 63545351 Eya1_peak_2681 123 . 9.02417 17.29891 12.38175 147 chr17 3115300 3115413 Eya1_peak_1618 123 . 9.02417 17.29891 12.38175 42 chr13 17695529 17695696 Eya1_peak_1038 123 . 9.02417 17.29891 12.38175 103 chr11 81115800 81115945 Eya1_peak_670 123 . 9.29675 17.21804 12.30533 80 chr11 77607492 77607821 Eya1_peak_641 123 . 9.29675 17.21804 12.30533 221 chr8 70352939 70353143 Eya1_peak_3746 122 . 8.96931 17.20944 12.29809 156 chr2 118779677 118779766 Eya1_peak_2263 122 . 8.64114 17.19051 12.27938 60 chr11 78496009 78496134 Eya1_peak_657 122 . 8.64114 17.19051 12.27938 90 chr11 69395849 69396010 Eya1_peak_587 122 . 8.64114 17.19051 12.27938 66 chr5 33820797 33821103 Eya1_peak_2925 122 . 8.94213 17.16508 12.25664 128 chr11 120990565 120991048 Eya1_peak_853 122 . 8.91511 17.12097 12.21316 403 chr4 103875698 103875848 Eya1_peak_2715 121 . 9.20561 17.07150 12.16613 63 chr15 81585528 81585803 Eya1_peak_1432 121 . 9.20561 17.07150 12.16613 168 chr12 70974783 70974991 Eya1_peak_932 121 . 8.86156 17.03346 12.12892 127 chr7 114254302 114254718 Eya1_peak_3583 121 . 9.17562 17.02327 12.11888 71 chr2 43613685 43613824 Eya1_peak_2157 121 . 9.17562 17.02327 12.11888 66 chr18 21001956 21002108 Eya1_peak_1839 121 . 9.17562 17.02327 12.11888 88 chr1 135634944 135635091 Eya1_peak_140 121 . 9.17562 17.02327 12.11888 36 chr11 104053376 104053512 Eya1_peak_777 120 . 9.11623 16.92770 12.02791 72 chr1 181210982 181211214 Eya1_peak_203 119 . 9.08682 16.88036 11.98119 171 chr5 65763280 65763833 Eya1_peak_2964 119 . 8.75638 16.86128 11.96287 69 chr4 124860577 124860745 Eya1_peak_2756 119 . 8.75638 16.86128 11.96287 34 chr18 34777065 34777558 Eya1_peak_1860 119 . 8.75638 16.86128 11.96287 217 chr2 158570515 158570602 Eya1_peak_2353 119 . 7.85213 16.85652 11.96075 38 chr9 121791342 121791495 Eya1_peak_4132 119 . 8.40568 16.79602 11.90165 83 chr2 69897412 69897853 Eya1_peak_2185 119 . 8.40568 16.79602 11.90165 381 chr10 119239112 119239548 Eya1_peak_398 119 . 8.40568 16.79602 11.90165 274 chrX 94122708 94123418 Eya1_peak_4150 118 . 9.34454 16.78158 11.88914 34 chr9 26727583 26727693 Eya1_peak_3912 118 . 9.34454 16.78158 11.88914 68 chr7 51621837 51621946 Eya1_peak_3500 118 . 9.34454 16.78158 11.88914 54 chr7 117021827 117021986 Eya1_peak_3586 118 . 9.34454 16.78158 11.88914 88 chr4 133753529 133753746 Eya1_peak_2808 118 . 8.70472 16.77656 11.88914 49 chr3 16183570 16183691 Eya1_peak_2435 118 . 9.34454 16.78158 11.88914 66 chr19 22139293 22139436 Eya1_peak_2009 118 . 9.34454 16.78158 11.88914 70 chr1 79440002 79440146 Eya1_peak_80 118 . 9.34454 16.78158 11.88914 18 chr17 48917557 48917644 Eya1_peak_1756 118 . 9.34454 16.78158 11.88914 53 chr16 39985141 39985250 Eya1_peak_1571 118 . 9.34454 16.78158 11.88914 47 chr12 106633218 106633338 Eya1_peak_1001 118 . 9.34454 16.78158 11.88914 88 chr12 102949728 102949830 Eya1_peak_995 118 . 9.34454 16.78158 11.88914 64 chr11 66259009 66259091 Eya1_peak_577 118 . 9.34454 16.78158 11.88914 37 chr10 94305644 94305759 Eya1_peak_374 118 . 9.34454 16.78158 11.88914 54 chr10 34282286 34282614 Eya1_peak_248 118 . 9.34454 16.78158 11.88914 71 chr2 163439324 163439404 Eya1_peak_2365 118 . 8.99972 16.74006 11.85498 38 chr2 166995940 166996230 Eya1_peak_2384 118 . 9.31572 16.73557 11.85117 136 chr17 47502085 47502280 Eya1_peak_1752 118 . 8.97106 16.69386 11.81013 107 chr10 91384430 91384516 Eya1_peak_369 118 . 8.97106 16.69386 11.81013 36 chr8 9309608 9309725 Eya1_peak_3684 118 . 9.28348 16.68411 11.80132 65 chr17 42876172 42876330 Eya1_peak_1731 118 . 9.28348 16.68411 11.80132 97 chr2 156111392 156111766 Eya1_peak_2333 117 . 8.94258 16.64793 11.76582 294 chr11 82313250 82313387 Eya1_peak_673 117 . 9.21968 16.58225 11.70153 87 chr7 82625451 82625609 Eya1_peak_3536 116 . 8.88615 16.55691 11.67658 59 chr6 83914707 83914860 Eya1_peak_3292 116 . 8.88615 16.55691 11.67658 83 chr19 12794978 12795064 Eya1_peak_2004 116 . 8.88615 16.55691 11.67658 38 chr9 45710577 45710656 Eya1_peak_3936 116 . 9.18810 16.53184 11.65467 40 chr12 65036330 65036797 Eya1_peak_916 116 . 9.18810 16.53184 11.65467 255 chr11 77930844 77931116 Eya1_peak_646 115 . 8.50402 16.44647 11.57114 72 chr2 26933085 26933311 Eya1_peak_2105 115 . 8.18271 16.41961 11.54750 161 chr4 116075436 116076501 Eya1_peak_2734 115 . 6.85236 16.40859 11.53696 749 chr3 90052011 90052399 Eya1_peak_2499 115 . 6.85236 16.40859 11.53696 168 chr13 54945433 54945584 Eya1_peak_1103 115 . 6.85236 16.40859 11.53696 83 chr11 103656673 103656822 Eya1_peak_775 115 . 6.85236 16.40859 11.53696 60 chr5 146360502 146360631 Eya1_peak_3168 115 . 9.09466 16.38267 11.51420 64 chr17 88064645 88065554 Eya1_peak_1813 115 . 9.09466 16.38267 11.51420 519 chr12 113098409 113098918 Eya1_peak_1021 114 . 8.74816 16.33397 11.46691 341 chr8 8690201 8690526 Eya1_peak_3683 114 . 7.83232 16.31975 11.45305 262 chr7 111081802 111082617 Eya1_peak_3574 114 . 7.83232 16.31975 11.45305 671 chr5 62483689 62483780 Eya1_peak_2954 114 . 7.83232 16.31975 11.45305 39 chr4 44704397 44704585 Eya1_peak_2653 114 . 7.83232 16.31975 11.45305 82 chr3 58576721 58577073 Eya1_peak_2467 114 . 7.83232 16.31975 11.45305 192 chr2 25982729 25983067 Eya1_peak_2100 114 . 7.83232 16.31975 11.45305 70 chr2 152414284 152414517 Eya1_peak_2309 114 . 7.83232 16.31975 11.45305 169 chr17 7741124 7741260 Eya1_peak_1631 114 . 7.83232 16.31975 11.45305 55 chr5 121009542 121009704 Eya1_peak_3069 114 . 9.03341 16.28488 11.43014 59 chr14 73142996 73143427 Eya1_peak_1312 114 . 9.03341 16.28488 11.43014 181 chr10 80748721 80748926 Eya1_peak_335 113 . 8.69416 16.24659 11.39406 114 chr11 32455058 32455319 Eya1_peak_490 113 . 9.00309 16.23647 11.38449 145 chr8 33929426 33929771 Eya1_peak_3716 112 . 8.94307 16.14061 11.29036 188 chr1 84838926 84839180 Eya1_peak_87 112 . 8.94307 16.14061 11.29036 126 chr17 4994503 4994618 Eya1_peak_1622 112 . 8.94307 16.14061 11.29036 55 chr1 63614752 63614856 Eya1_peak_60 112 . 8.94307 16.14061 11.29036 53 chr9 102625719 102625850 Eya1_peak_4064 112 . 8.61440 16.11738 11.26846 46 chr16 8830721 8830969 Eya1_peak_1506 112 . 8.61440 16.11738 11.26846 98 chr12 85339017 85339364 Eya1_peak_969 112 . 8.61440 16.11738 11.26846 234 chr11 58009167 58009458 Eya1_peak_553 112 . 8.61440 16.11738 11.26846 60 chr10 58446881 58447295 Eya1_peak_277 112 . 8.61440 16.11738 11.26846 327 chr12 54862361 54862611 Eya1_peak_904 112 . 8.91336 16.09314 11.24820 174 chr19 45097977 45098097 Eya1_peak_2042 112 . 8.26581 16.05236 11.20937 49 chr15 96287006 96287243 Eya1_peak_1464 112 . 8.88384 16.04598 11.20494 97 chr11 32642853 32643190 Eya1_peak_491 111 . 8.56203 16.03245 11.19274 215 chr11 35769754 35770209 Eya1_peak_501 111 . 8.85452 15.99913 11.15977 170 chr11 20201474 20201943 Eya1_peak_467 111 . 8.85452 15.99913 11.15977 236 chr1 74392026 74392286 Eya1_peak_69 111 . 8.53608 15.99034 11.15266 51 chr6 71271638 71271928 Eya1_peak_3276 110 . 8.79646 15.90631 11.07115 253 chr17 34899043 34899592 Eya1_peak_1705 110 . 8.79646 15.90631 11.07115 201 chr9 113741240 113741388 Eya1_peak_4111 110 . 8.76771 15.86034 11.02677 94 chr7 109129581 109129672 Eya1_peak_3566 109 . 8.73915 15.81466 10.98217 39 chr3 135438984 135439397 Eya1_peak_2566 109 . 8.73915 15.81466 10.98217 105 chr2 91526817 91527208 Eya1_peak_2219 109 . 8.73915 15.81466 10.98217 70 chr17 84958048 84958153 Eya1_peak_1808 109 . 8.73915 15.81466 10.98217 50 chr12 92040610 92040719 Eya1_peak_981 109 . 8.73915 15.81466 10.98217 41 chr11 51263355 51263496 Eya1_peak_524 109 . 8.71077 15.76926 10.94092 83 chr8 19980100 19980287 Eya1_peak_3698 108 . 6.74269 15.72432 10.89659 132 chr10 62791761 62792101 Eya1_peak_290 108 . 7.77047 15.71528 10.88817 218 chr5 116545913 116546006 Eya1_peak_3054 108 . 8.35876 15.70195 10.87493 36 chr1 4857782 4858014 Eya1_peak_2 108 . 8.35876 15.70195 10.87493 130 chr14 47649411 47649798 Eya1_peak_1263 108 . 8.35876 15.70195 10.87493 319 chr14 34673914 34674413 Eya1_peak_1251 108 . 8.35876 15.70195 10.87493 353 chr13 98316480 98316913 Eya1_peak_1172 108 . 8.35876 15.70195 10.87493 148 chr5 88675466 88675669 Eya1_peak_2987 108 . 8.65457 15.67932 10.85590 118 chr1 167187921 167188027 Eya1_peak_183 108 . 8.65457 15.67932 10.85590 47 chr12 80112205 80112568 Eya1_peak_946 108 . 8.04057 15.67711 10.85434 94 chr6 31398837 31399374 Eya1_peak_3208 108 . 8.62674 15.63476 10.81378 251 chr5 147430822 147431249 Eya1_peak_3174 108 . 8.62674 15.63476 10.81378 62 chr5 116554041 116554146 Eya1_peak_3055 108 . 8.62674 15.63476 10.81378 48 chr8 33386049 33386187 Eya1_peak_3712 107 . 8.87783 15.54125 10.72335 51 chr6 8209454 8209590 Eya1_peak_3188 107 . 8.87783 15.54125 10.72335 52 chr4 14145576 14145715 Eya1_peak_2616 107 . 8.87783 15.54125 10.72335 72 chr3 16183292 16183469 Eya1_peak_2434 107 . 8.87783 15.54125 10.72335 77 chr2 94524683 94524781 Eya1_peak_2235 107 . 8.87783 15.54125 10.72335 50 chr17 39129231 39129356 Eya1_peak_1721 107 . 8.87783 15.54125 10.72335 52 chr16 62758479 62758601 Eya1_peak_1586 107 . 8.87783 15.54125 10.72335 58 chr1 3670709 3670908 Eya1_peak_1 107 . 8.87783 15.54125 10.72335 128 chr12 70347180 70347333 Eya1_peak_930 107 . 8.87783 15.54125 10.72335 63 chr12 5717647 5717738 Eya1_peak_865 107 . 8.87783 15.54125 10.72335 46 chr1 159702166 159702307 Eya1_peak_169 107 . 8.87783 15.54125 10.72335 50 chr10 6788819 6788922 Eya1_peak_223 107 . 8.87783 15.54125 10.72335 59 chr4 151995612 151995908 Eya1_peak_2868 106 . 8.54432 15.50271 10.69313 246 chr11 57434298 57434411 Eya1_peak_551 106 . 8.85045 15.49779 10.68930 42 chr8 105496924 105497056 Eya1_peak_3825 106 . 8.51719 15.45923 10.65137 93 chr17 46383835 46383943 Eya1_peak_1742 106 . 8.51719 15.45923 10.65137 46 chr11 84944041 84944219 Eya1_peak_685 106 . 8.51719 15.45923 10.65137 65 chr6 33126717 33126854 Eya1_peak_3213 106 . 6.60783 15.45244 10.64507 54 chr2 24762018 24762151 Eya1_peak_2092 106 . 6.60783 15.45244 10.64507 78 chr17 25273508 25274020 Eya1_peak_1655 106 . 6.60783 15.45244 10.64507 209 chr17 25272890 25273340 Eya1_peak_1654 106 . 6.60783 15.45244 10.64507 308 chr13 58402234 58402449 Eya1_peak_1130 106 . 6.60783 15.45244 10.64507 97 chr7 120426818 120426891 Eya1_peak_3594 106 . 8.81983 15.44919 10.64485 25 chr15 87887164 87887242 Eya1_peak_1450 106 . 8.81983 15.44919 10.64485 28 chr12 104751342 104751762 Eya1_peak_996 106 . 8.49024 15.41600 10.61249 348 chr6 52713754 52714160 Eya1_peak_3267 105 . 8.46345 15.37303 10.57051 315 chr2 18064653 18064972 Eya1_peak_2079 105 . 8.75921 15.35299 10.55392 209 chr17 63499463 63500102 Eya1_peak_1768 105 . 8.75921 15.35299 10.55392 543 chr16 9836669 9836762 Eya1_peak_1508 105 . 8.75921 15.35299 10.55392 62 chr11 21238849 21239621 Eya1_peak_475 105 . 8.43684 15.33032 10.53203 65 chr3 103573908 103574051 Eya1_peak_2533 105 . 7.82729 15.31911 10.52166 42 chr15 76477536 76477660 Eya1_peak_1401 105 . 7.82729 15.31911 10.52166 65 chr3 8508196 8508289 Eya1_peak_2428 105 . 8.11787 15.30826 10.51147 35 chr2 180920570 180920714 Eya1_peak_2421 105 . 8.11787 15.30826 10.51147 50 chr19 8820233 8820597 Eya1_peak_1992 105 . 8.72921 15.30538 10.51147 258 chr12 86994360 86994448 Eya1_peak_974 105 . 8.11787 15.30826 10.51147 45 chr11 52232093 52232236 Eya1_peak_533 105 . 8.11787 15.30826 10.51147 95 chr8 46740768 46741019 Eya1_peak_3727 104 . 8.41039 15.28786 10.49512 92 chr7 120917895 120918344 Eya1_peak_3596 104 . 8.69941 15.25811 10.46585 114 chr4 62257084 62257219 Eya1_peak_2677 104 . 8.69941 15.25811 10.46585 44 chr9 72662458 72663089 Eya1_peak_4020 104 . 7.50627 15.25735 10.46552 459 chr9 119706827 119706971 Eya1_peak_4124 104 . 7.50627 15.25735 10.46552 61 chr8 71671663 71671813 Eya1_peak_3752 104 . 7.50627 15.25735 10.46552 49 chr7 25754078 25754770 Eya1_peak_3439 104 . 7.50627 15.25735 10.46552 485 chr7 16183792 16183984 Eya1_peak_3411 104 . 7.50627 15.25735 10.46552 116 chr6 29735700 29736347 Eya1_peak_3201 104 . 7.50627 15.25735 10.46552 340 chr5 113716718 113716909 Eya1_peak_3037 104 . 7.50627 15.25735 10.46552 59 chr4 117893529 117893660 Eya1_peak_2739 104 . 7.50627 15.25735 10.46552 63 chr3 51416159 51416724 Eya1_peak_2459 104 . 7.50627 15.25735 10.46552 454 chr2 154892374 154892729 Eya1_peak_2321 104 . 7.50627 15.25735 10.46552 193 chr2 109675985 109676095 Eya1_peak_2249 104 . 7.50627 15.25735 10.46552 58 chr19 42397410 42397579 Eya1_peak_2035 104 . 7.50627 15.25735 10.46552 91 chr19 37207649 37208143 Eya1_peak_2024 104 . 7.50627 15.25735 10.46552 198 chr1 93272616 93272762 Eya1_peak_103 104 . 7.50627 15.25735 10.46552 91 chr14 75366893 75367015 Eya1_peak_1314 104 . 7.50627 15.25735 10.46552 62 chr13 42711668 42711814 Eya1_peak_1080 104 . 7.50627 15.25735 10.46552 76 chr13 105442714 105442844 Eya1_peak_1184 104 . 7.50627 15.25735 10.46552 65 chr11 12025851 12026021 Eya1_peak_461 104 . 7.50627 15.25735 10.46552 45 chr11 103132311 103132684 Eya1_peak_774 104 . 7.50627 15.25735 10.46552 305 chr10 81477668 81477831 Eya1_peak_348 104 . 7.50627 15.25735 10.46552 50 chr10 76958348 76958430 Eya1_peak_306 104 . 7.50627 15.25735 10.46552 34 chr16 20517215 20517397 Eya1_peak_1538 104 . 8.38411 15.24564 10.46501 93 chr9 108517096 108517263 Eya1_peak_4093 104 . 8.66982 15.21115 10.43159 127 chr11 84724269 84724380 Eya1_peak_681 104 . 8.66982 15.21115 10.43159 62 chr8 95806773 95807075 Eya1_peak_3813 103 . 8.33203 15.16196 10.38554 228 chr7 44593893 44594090 Eya1_peak_3483 103 . 5.87314 15.16215 10.38554 117 chr14 68125671 68125796 Eya1_peak_1306 103 . 5.87314 15.16215 10.38554 61 chr16 8737936 8738395 Eya1_peak_1503 103 . 8.61124 15.11818 10.34302 27 chr1 159524227 159524358 Eya1_peak_167 103 . 8.61124 15.11818 10.34302 62 chr11 96005522 96005855 Eya1_peak_724 103 . 8.28059 15.07923 10.30452 63 chr11 118659410 118659517 Eya1_peak_834 103 . 8.28059 15.07923 10.30452 72 chr9 98234883 98234980 Eya1_peak_4053 102 . 8.58224 15.07216 10.29779 37 chr4 8535721 8535997 Eya1_peak_2606 102 . 8.58224 15.07216 10.29779 204 chr16 5765282 5765409 Eya1_peak_1500 102 . 8.58224 15.07216 10.29779 72 chr11 106084637 106085384 Eya1_peak_786 102 . 8.58224 15.07216 10.29779 52 chr15 76351434 76351512 Eya1_peak_1400 102 . 7.39777 15.06764 10.29579 28 chr7 30346761 30346943 Eya1_peak_3457 102 . 8.55344 15.02645 10.25587 55 chr17 6490667 6490839 Eya1_peak_1630 102 . 7.64478 15.01049 10.24059 116 chr4 123664106 123664436 Eya1_peak_2748 102 . 8.22979 14.99745 10.22758 261 chr8 78508485 78508893 Eya1_peak_3761 102 . 7.62502 14.97695 10.20832 67 chr5 35299759 35299877 Eya1_peak_2933 102 . 7.62502 14.97695 10.20832 55 chr8 95028537 95028634 Eya1_peak_3811 101 . 8.20462 14.95691 10.18869 46 chr6 32710303 32710467 Eya1_peak_3212 101 . 8.20462 14.95691 10.18869 63 chr6 117908047 117908287 Eya1_peak_3350 101 . 8.20462 14.95691 10.18869 34 chr14 62760578 62760815 Eya1_peak_1294 101 . 8.20462 14.95691 10.18869 49 chr12 87471904 87472212 Eya1_peak_977 101 . 8.20462 14.95691 10.18869 220 chr11 98324122 98324254 Eya1_peak_745 101 . 8.20462 14.95691 10.18869 77 chr11 4750371 4750579 Eya1_peak_446 101 . 8.20462 14.95691 10.18869 54 chr10 11081594 11081712 Eya1_peak_234 101 . 8.20462 14.95691 10.18869 66 chr4 99194016 99194120 Eya1_peak_2704 101 . 7.89047 14.93427 10.17177 54 chr16 8830189 8830643 Eya1_peak_1505 101 . 7.89047 14.93427 10.17177 113 chr17 29614921 29615084 Eya1_peak_1680 101 . 8.46819 14.89111 10.13131 58 chr14 66909853 66909969 Eya1_peak_1305 101 . 8.46819 14.89111 10.13131 50 chr7 123503469 123503594 Eya1_peak_3608 100 . 8.44015 14.84658 10.08846 55 chr5 115429751 115430116 Eya1_peak_3046 100 . 8.44015 14.84658 10.08846 216 chr4 86748804 86749234 Eya1_peak_2690 100 . 8.44015 14.84658 10.08846 183 chr4 46451555 46452189 Eya1_peak_2656 100 . 8.13003 14.83664 10.07938 412 chr5 44226847 44227098 Eya1_peak_2947 100 . 8.10547 14.79700 10.04169 157 chr16 23107825 23107987 Eya1_peak_1547 100 . 8.10547 14.79700 10.04169 53 chr15 82921205 82921352 Eya1_peak_1436 100 . 8.10547 14.79700 10.04169 113 chr7 45216116 45216230 Eya1_peak_3491 100 . 8.08105 14.75757 10.00387 63 chr5 148070074 148070179 Eya1_peak_3175 100 . 8.38462 14.75838 10.00387 50 chr10 42761653 42762124 Eya1_peak_262 100 . 8.38462 14.75838 10.00387 344 chr4 123664574 123664700 Eya1_peak_2749 99 . 8.05678 14.71837 9.96534 35 chr18 61555400 61555923 Eya1_peak_1901 99 . 8.03266 14.67938 9.92753 257 chr9 72532543 72532694 Eya1_peak_4019 99 . 8.32981 14.67130 9.91958 56 chr12 3807921 3808058 Eya1_peak_860 99 . 8.32981 14.67130 9.91958 96 chr1 127774305 127774661 Eya1_peak_117 99 . 8.32981 14.67130 9.91958 198 chr8 79398852 79398963 Eya1_peak_3766 98 . 8.30268 14.62818 9.87771 60 chr5 112575575 112575710 Eya1_peak_3031 98 . 8.30268 14.62818 9.87771 64 chr3 146812637 146812898 Eya1_peak_2585 98 . 8.30268 14.62818 9.87771 103 chr19 3767624 3767729 Eya1_peak_1946 98 . 8.30268 14.62818 9.87771 40 chr16 23890281 23890385 Eya1_peak_1548 98 . 8.30268 14.62818 9.87771 55 chr1 55027097 55027348 Eya1_peak_40 98 . 8.30268 14.62818 9.87771 179 chr14 34502915 34503100 Eya1_peak_1249 98 . 8.30268 14.62818 9.87771 56 chr13 14613291 14613662 Eya1_peak_1036 98 . 8.30268 14.62818 9.87771 52 chr11 58009527 58009873 Eya1_peak_554 98 . 8.30268 14.62818 9.87771 195 chr11 23307064 23307204 Eya1_peak_480 98 . 8.30268 14.62818 9.87771 39 chr9 21546938 21547136 Eya1_peak_3904 98 . 8.27572 14.58532 9.83922 44 chr7 3645651 3645829 Eya1_peak_3392 98 . 8.27572 14.58532 9.83922 37 chr7 127614997 127615257 Eya1_peak_3635 98 . 8.27572 14.58532 9.83922 99 chr8 3279402 3279522 Eya1_peak_3677 98 . 7.67546 14.57825 9.83308 67 chr2 31759994 31760349 Eya1_peak_2128 98 . 7.67546 14.57825 9.83308 265 chr19 45659796 45660362 Eya1_peak_2043 98 . 7.67546 14.57825 9.83308 354 chr6 48086118 48086480 Eya1_peak_3246 98 . 7.96115 14.56367 9.82017 99 chr5 27366082 27366208 Eya1_peak_2904 98 . 7.96115 14.56367 9.82017 48 chr5 117264875 117264980 Eya1_peak_3060 98 . 7.96115 14.56367 9.82017 53 chr5 116829931 116830089 Eya1_peak_3058 98 . 7.96115 14.56367 9.82017 41 chr4 44434730 44434828 Eya1_peak_2650 98 . 7.96115 14.56367 9.82017 55 chr17 24550113 24550460 Eya1_peak_1649 98 . 7.96115 14.56367 9.82017 124 chr6 83927572 83927689 Eya1_peak_3293 97 . 6.36330 14.51252 9.77333 66 chr14 50720002 50720159 Eya1_peak_1269 97 . 6.36330 14.51252 9.77333 106 chr12 84698611 84698781 Eya1_peak_965 97 . 6.36330 14.51252 9.77333 72 chr11 55897637 55897811 Eya1_peak_549 97 . 6.36330 14.51252 9.77333 62 chr10 71428393 71428502 Eya1_peak_301 97 . 6.36330 14.51252 9.77333 43 chr15 84109066 84109254 Eya1_peak_1441 97 . 8.22233 14.50041 9.76486 33 chr2 165160594 165160713 Eya1_peak_2379 97 . 8.19589 14.45834 9.72388 39 chr19 42326040 42326167 Eya1_peak_2034 97 . 8.19589 14.45834 9.72388 58 chr15 12118467 12118725 Eya1_peak_1351 97 . 8.19589 14.45834 9.72388 26 chr13 55714733 55714869 Eya1_peak_1117 96 . 8.16962 14.41654 9.68337 86 chr7 116093352 116093611 Eya1_peak_3585 96 . 8.14352 14.37499 9.64277 165 chr4 133752611 133753045 Eya1_peak_2805 96 . 7.84476 14.37492 9.64277 40 chr18 73572878 73573418 Eya1_peak_1914 96 . 8.14352 14.37499 9.64277 433 chr11 116852169 116852251 Eya1_peak_824 96 . 8.14352 14.37499 9.64277 23 chr4 151185895 151185986 Eya1_peak_2860 96 . 7.25032 14.33534 9.60425 41 chr9 52168033 52168537 Eya1_peak_3950 96 . 8.11758 14.33369 9.60280 448 chr10 117375918 117376429 Eya1_peak_394 96 . 8.11758 14.33369 9.60280 391 chr7 124742213 124742340 Eya1_peak_3610 95 . 8.41113 14.32425 9.59446 60 chr4 44260459 44260599 Eya1_peak_2649 95 . 8.41113 14.32425 9.59446 87 chr4 3835260 3835617 Eya1_peak_2600 95 . 8.41113 14.32425 9.59446 177 chr2 165687656 165687746 Eya1_peak_2381 95 . 8.41113 14.32425 9.59446 41 chr2 162031748 162031852 Eya1_peak_2360 95 . 8.41113 14.32425 9.59446 46 chr19 21272999 21273084 Eya1_peak_2008 95 . 8.41113 14.32425 9.59446 46 chr18 6765430 6765592 Eya1_peak_1823 95 . 8.41113 14.32425 9.59446 94 chr15 101879892 101880025 Eya1_peak_1487 95 . 8.41113 14.32425 9.59446 52 chr12 105785065 105785199 Eya1_peak_999 95 . 8.41113 14.32425 9.59446 65 chr9 119149701 119149869 Eya1_peak_4119 95 . 5.67752 14.29954 9.57879 71 chr5 116591454 116591613 Eya1_peak_3056 95 . 5.67752 14.29954 9.57879 68 chr5 65537749 65537982 Eya1_peak_2962 95 . 8.09181 14.29264 9.57239 47 chr5 108694508 108694603 Eya1_peak_3021 95 . 8.09181 14.29264 9.57239 60 chr3 27370242 27370442 Eya1_peak_2440 95 . 8.09181 14.29264 9.57239 114 chr12 8674445 8674843 Eya1_peak_868 95 . 8.09181 14.29264 9.57239 147 chr8 105636947 105637176 Eya1_peak_3828 95 . 8.06620 14.25184 9.53325 203 chr9 110116953 110117364 Eya1_peak_4102 95 . 7.47186 14.23865 9.52050 223 chr5 142694732 142694862 Eya1_peak_3153 95 . 7.47186 14.23865 9.52050 89 chr13 111687109 111687234 Eya1_peak_1192 95 . 8.35617 14.23760 9.52017 61 chr9 61373039 61373135 Eya1_peak_3987 94 . 7.18023 14.21410 9.49742 30 chr9 46980283 46980372 Eya1_peak_3941 94 . 7.18023 14.21410 9.49742 40 chr7 28505735 28505819 Eya1_peak_3450 94 . 7.18023 14.21410 9.49742 32 chr7 12478390 12478871 Eya1_peak_3404 94 . 7.18023 14.21410 9.49742 158 chr6 113962914 113963004 Eya1_peak_3337 94 . 7.18023 14.21410 9.49742 52 chr5 65697118 65697760 Eya1_peak_2963 94 . 7.18023 14.21410 9.49742 114 chr5 37257373 37257507 Eya1_peak_2941 94 . 7.18023 14.21410 9.49742 63 chr5 142906154 142906701 Eya1_peak_3157 94 . 7.18023 14.21410 9.49742 276 chr5 129287599 129287710 Eya1_peak_3110 94 . 8.04075 14.21128 9.49742 59 chr5 122264129 122264407 Eya1_peak_3079 94 . 7.18023 14.21410 9.49742 149 chr5 115272343 115272653 Eya1_peak_3045 94 . 7.18023 14.21410 9.49742 239 chr4 138325837 138326036 Eya1_peak_2831 94 . 7.18023 14.21410 9.49742 83 chr4 132308767 132308956 Eya1_peak_2799 94 . 7.18023 14.21410 9.49742 125 chr3 55112166 55112349 Eya1_peak_2461 94 . 8.04075 14.21128 9.49742 54 chr3 135438801 135438909 Eya1_peak_2565 94 . 8.04075 14.21128 9.49742 46 chr2 178735197 178735363 Eya1_peak_2406 94 . 8.04075 14.21128 9.49742 63 chr1 99772342 99772459 Eya1_peak_108 94 . 7.18023 14.21410 9.49742 47 chr18 76853220 76853304 Eya1_peak_1925 94 . 7.18023 14.21410 9.49742 15 chr17 37046227 37046347 Eya1_peak_1719 94 . 7.18023 14.21410 9.49742 53 chr17 30005167 30005259 Eya1_peak_1682 94 . 8.04075 14.21128 9.49742 35 chr16 18288859 18289209 Eya1_peak_1533 94 . 8.04075 14.21128 9.49742 68 chr15 102670791 102670985 Eya1_peak_1493 94 . 7.18023 14.21410 9.49742 55 chr1 5022813 5022938 Eya1_peak_4 94 . 7.18023 14.21410 9.49742 59 chr13 98925692 98926645 Eya1_peak_1173 94 . 7.18023 14.21410 9.49742 372 chr13 58663435 58663596 Eya1_peak_1131 94 . 7.18023 14.21410 9.49742 97 chr13 34875606 34875946 Eya1_peak_1072 94 . 8.04075 14.21128 9.49742 127 chr11 94321458 94321749 Eya1_peak_713 94 . 7.18023 14.21410 9.49742 237 chr1 176697237 176697317 Eya1_peak_189 94 . 7.18023 14.21410 9.49742 31 chr1 17145551 17145678 Eya1_peak_14 94 . 7.18023 14.21410 9.49742 59 chr11 69671974 69672214 Eya1_peak_590 94 . 8.04075 14.21128 9.49742 97 chr11 104114853 104114970 Eya1_peak_778 94 . 7.18023 14.21410 9.49742 49 chr11 102184781 102184881 Eya1_peak_762 94 . 7.18023 14.21410 9.49742 29 chr10 45546997 45547078 Eya1_peak_268 94 . 7.18023 14.21410 9.49742 34 chr10 128083331 128083762 Eya1_peak_419 94 . 7.18023 14.21410 9.49742 135 chr4 128727690 128728021 Eya1_peak_2776 94 . 8.32736 14.19217 9.49134 261 chr4 101550800 101550881 Eya1_peak_2709 94 . 8.32736 14.19217 9.49134 58 chr15 86544202 86544369 Eya1_peak_1448 94 . 8.32736 14.19217 9.49134 47 chr8 13339019 13339293 Eya1_peak_3695 94 . 7.73171 14.19107 9.49076 232 chr7 10325757 10325837 Eya1_peak_3403 94 . 7.73171 14.19107 9.49076 53 chr4 87221697 87221826 Eya1_peak_2692 94 . 7.73171 14.19107 9.49076 59 chr14 26970310 26970434 Eya1_peak_1226 94 . 7.73171 14.19107 9.49076 64 chr11 97279886 97280535 Eya1_peak_732 94 . 8.01547 14.17096 9.47363 525 chr10 81136954 81137158 Eya1_peak_342 94 . 7.68740 14.11886 9.42402 38 chr3 80802944 80803070 Eya1_peak_2481 94 . 8.27032 14.10225 9.40771 48 chr11 78165132 78165323 Eya1_peak_653 93 . 7.96537 14.09104 9.39697 65 chr2 125858693 125858923 Eya1_peak_2279 93 . 8.24209 14.05775 9.36464 64 chr4 152424499 152424609 Eya1_peak_2871 93 . 7.94055 14.05143 9.35918 53 chr2 73910675 73910993 Eya1_peak_2195 93 . 7.94055 14.05143 9.35918 195 chr15 98871209 98871374 Eya1_peak_1479 93 . 7.94055 14.05143 9.35918 119 chr11 98795776 98796170 Eya1_peak_750 93 . 7.94055 14.05143 9.35918 270 chr14 104453991 104454087 Eya1_peak_1334 93 . 8.21405 14.01356 9.32344 36 chr5 148928812 148928938 Eya1_peak_3178 93 . 7.91589 14.01206 9.32283 63 chr13 94976389 94976594 Eya1_peak_1169 92 . 7.89138 13.97291 9.28429 39 chr2 32151274 32151542 Eya1_peak_2130 92 . 7.86703 13.93398 9.24690 203 chr19 5801116 5801388 Eya1_peak_1972 92 . 7.86703 13.93398 9.24690 99 chr16 20619983 20620081 Eya1_peak_1540 92 . 8.15855 13.92607 9.23962 32 chr3 130060421 130060620 Eya1_peak_2564 92 . 7.27878 13.91415 9.22865 44 chr5 108549640 108549747 Eya1_peak_3020 91 . 8.13108 13.88277 9.19855 43 chr19 41263723 41263998 Eya1_peak_2028 91 . 8.13108 13.88277 9.19855 43 chr1 58423732 58423886 Eya1_peak_48 91 . 8.13108 13.88277 9.19855 14 chr13 54260412 54260488 Eya1_peak_1095 91 . 8.13108 13.88277 9.19855 40 chr12 108178806 108179249 Eya1_peak_1003 91 . 8.13108 13.88277 9.19855 380 chr10 125966795 125966869 Eya1_peak_408 91 . 8.13108 13.88277 9.19855 24 chr6 47748613 47748855 Eya1_peak_3238 91 . 3.75131 13.87458 9.19366 181 chr10 5639265 5639357 Eya1_peak_221 91 . 8.10379 13.83975 9.15938 54 chr5 112824518 112824644 Eya1_peak_3033 91 . 7.51513 13.83721 9.15770 61 chr4 155812626 155812839 Eya1_peak_2884 91 . 7.51513 13.83721 9.15770 48 chr1 131910547 131910688 Eya1_peak_122 91 . 7.51513 13.83721 9.15770 78 chr9 119389101 119389237 Eya1_peak_4120 91 . 7.79485 13.81854 9.14080 60 chr8 91313531 91313763 Eya1_peak_3800 91 . 7.79485 13.81854 9.14080 92 chr8 84969988 84970085 Eya1_peak_3783 91 . 7.79485 13.81854 9.14080 57 chr6 28423754 28424002 Eya1_peak_3199 91 . 7.79485 13.81854 9.14080 99 chr4 108780054 108780347 Eya1_peak_2725 91 . 7.79485 13.81854 9.14080 70 chr2 92671844 92671931 Eya1_peak_2228 91 . 7.79485 13.81854 9.14080 35 chr15 81745500 81745748 Eya1_peak_1434 91 . 7.79485 13.81854 9.14080 18 chr11 3774704 3774885 Eya1_peak_442 91 . 7.79485 13.81854 9.14080 113 chr4 115887033 115887108 Eya1_peak_2733 90 . 7.74746 13.74267 9.07146 41 chr15 96288333 96288798 Eya1_peak_1468 90 . 8.02302 13.71240 9.04152 41 chr5 108461550 108461785 Eya1_peak_3019 90 . 7.99645 13.67050 9.00087 132 chr4 154466461 154466552 Eya1_peak_2878 90 . 7.99645 13.67050 9.00087 25 chr5 129725100 129725434 Eya1_peak_3111 89 . 7.97006 13.62887 8.96126 101 chr2 155692048 155692197 Eya1_peak_2330 89 . 7.97006 13.62887 8.96126 46 chr17 74528676 74528914 Eya1_peak_1792 89 . 7.97006 13.62887 8.96126 191 chr4 126255818 126255937 Eya1_peak_2764 89 . 7.09543 13.60354 8.93701 87 chr3 107695942 107696050 Eya1_peak_2545 89 . 7.09543 13.60354 8.93701 63 chr11 98027006 98027104 Eya1_peak_739 89 . 7.09543 13.60354 8.93701 32 chr16 91011566 91011667 Eya1_peak_1599 89 . 7.65440 13.59345 8.92758 54 chr9 57468141 57468242 Eya1_peak_3967 89 . 6.11877 13.58947 8.92401 63 chr7 34702894 34703009 Eya1_peak_3470 89 . 6.11877 13.58947 8.92401 55 chr19 5087879 5088094 Eya1_peak_1957 89 . 6.11877 13.58947 8.92401 156 chr5 24357559 24357689 Eya1_peak_2895 88 . 5.05731 13.55013 8.88988 60 chr9 61914179 61914432 Eya1_peak_3989 88 . 7.91779 13.54641 8.88630 57 chr6 85498317 85498404 Eya1_peak_3298 88 . 7.91779 13.54641 8.88630 44 chr11 44519028 44519137 Eya1_peak_507 88 . 7.91779 13.54641 8.88630 39 chr5 33275343 33275423 Eya1_peak_2923 88 . 7.89192 13.50558 8.84671 62 chr15 96287875 96288071 Eya1_peak_1466 88 . 7.89192 13.50558 8.84671 138 chr1 37299945 37300177 Eya1_peak_27 88 . 7.89192 13.50558 8.84671 165 chr4 12140336 12140462 Eya1_peak_2613 88 . 7.31035 13.50040 8.84253 77 chr8 57652377 57652569 Eya1_peak_3740 88 . 7.86621 13.46501 8.80860 83 chr8 57652205 57652323 Eya1_peak_3739 88 . 7.86621 13.46501 8.80860 78 chr5 137510568 137510718 Eya1_peak_3139 88 . 7.86621 13.46501 8.80860 34 chr5 130363920 130364012 Eya1_peak_3115 88 . 7.86621 13.46501 8.80860 44 chr17 69417396 69417616 Eya1_peak_1780 88 . 7.86621 13.46501 8.80860 176 chr16 17722676 17722907 Eya1_peak_1528 88 . 7.86621 13.46501 8.80860 207 chr12 101083008 101083211 Eya1_peak_989 88 . 7.86621 13.46501 8.80860 145 chr11 49846978 49847073 Eya1_peak_517 88 . 7.86621 13.46501 8.80860 32 chr11 36396432 36396567 Eya1_peak_504 88 . 7.86621 13.46501 8.80860 35 chr7 126949897 126950109 Eya1_peak_3620 87 . 5.48189 13.45200 8.79980 152 chr6 115178977 115179091 Eya1_peak_3339 87 . 5.48189 13.45200 8.79980 49 chr18 46525487 46525617 Eya1_peak_1886 87 . 7.56354 13.44748 8.79606 34 chr17 33760031 33760247 Eya1_peak_1693 87 . 7.56354 13.44748 8.79606 94 chr14 80157117 80157246 Eya1_peak_1325 87 . 7.56354 13.44748 8.79606 110 chr11 86544481 86544658 Eya1_peak_693 87 . 7.56354 13.44748 8.79606 107 chr11 77982944 77983382 Eya1_peak_647 87 . 7.56354 13.44748 8.79606 238 chr11 72607476 72607576 Eya1_peak_614 87 . 7.56354 13.44748 8.79606 48 chr11 107817340 107817443 Eya1_peak_802 87 . 7.56354 13.44748 8.79606 38 chr10 119239630 119239984 Eya1_peak_399 87 . 7.56354 13.44748 8.79606 112 chr11 62456770 62457118 Eya1_peak_573 87 . 7.84067 13.42469 8.77607 174 chr10 95563588 95563688 Eya1_peak_377 87 . 7.84067 13.42469 8.77607 40 chr6 134566464 134566690 Eya1_peak_3379 87 . 7.81529 13.38462 8.73728 156 chr14 122107132 122107474 Eya1_peak_1344 87 . 7.81529 13.38462 8.73728 219 chr1 134560615 134561030 Eya1_peak_132 87 . 7.81529 13.38462 8.73728 59 chr11 104468797 104469403 Eya1_peak_781 87 . 7.81529 13.38462 8.73728 335 chr10 61783434 61783637 Eya1_peak_283 87 . 7.81529 13.38462 8.73728 133 chr6 92091522 92091630 Eya1_peak_3318 86 . 7.79008 13.34480 8.69828 61 chr1 82839821 82840081 Eya1_peak_85 86 . 7.79008 13.34480 8.69828 114 chr6 47454213 47454344 Eya1_peak_3227 86 . 7.74014 13.26590 8.62225 99 chr5 31193310 31193714 Eya1_peak_2912 86 . 7.74014 13.26590 8.62225 162 chr13 94878448 94878525 Eya1_peak_1168 85 . 7.71541 13.22682 8.58422 33 chr10 81378075 81378148 Eya1_peak_346 85 . 7.71541 13.22682 8.58422 26 chr5 122501639 122501738 Eya1_peak_3080 85 . 7.40962 13.19949 8.55762 45 chr9 71485324 71485875 Eya1_peak_4014 85 . 6.85419 13.19086 8.54902 458 chr9 64340595 64341230 Eya1_peak_3999 85 . 6.85419 13.19086 8.54902 159 chr9 122701895 122702022 Eya1_peak_4135 85 . 6.85419 13.19086 8.54902 64 chr9 107381812 107381945 Eya1_peak_4082 85 . 6.85419 13.19086 8.54902 71 chr8 87087610 87087685 Eya1_peak_3792 85 . 6.85419 13.19086 8.54902 49 chr8 123891458 123891548 Eya1_peak_3875 85 . 7.69084 13.18797 8.54902 58 chr6 28982516 28982671 Eya1_peak_3200 85 . 6.85419 13.19086 8.54902 108 chr6 124740850 124741000 Eya1_peak_3363 85 . 6.85419 13.19086 8.54902 91 chr5 128879279 128879376 Eya1_peak_3107 85 . 7.11644 13.17920 8.54902 49 chr4 155018791 155018938 Eya1_peak_2879 85 . 6.85419 13.19086 8.54902 22 chr4 129335168 129335255 Eya1_peak_2781 85 . 7.11644 13.17920 8.54902 20 chr3 158036361 158036563 Eya1_peak_2599 85 . 6.85419 13.19086 8.54902 68 chr3 154819850 154819959 Eya1_peak_2596 85 . 6.85419 13.19086 8.54902 58 chr2 90917501 90917808 Eya1_peak_2216 85 . 6.85419 13.19086 8.54902 163 chr2 48948892 48949191 Eya1_peak_2161 85 . 6.85419 13.19086 8.54902 184 chr2 163564807 163564883 Eya1_peak_2366 85 . 6.85419 13.19086 8.54902 32 chr2 160646116 160646866 Eya1_peak_2356 85 . 6.85419 13.19086 8.54902 272 chr2 130178906 130179253 Eya1_peak_2291 85 . 6.85419 13.19086 8.54902 173 chr19 60790326 60790511 Eya1_peak_2069 85 . 6.85419 13.19086 8.54902 125 chr1 84696318 84696436 Eya1_peak_86 85 . 6.85419 13.19086 8.54902 46 chr18 32163220 32163485 Eya1_peak_1853 85 . 6.85419 13.19086 8.54902 187 chr16 22265486 22265895 Eya1_peak_1546 85 . 6.85419 13.19086 8.54902 223 chr14 57889785 57890119 Eya1_peak_1291 85 . 6.85419 13.19086 8.54902 280 chr14 49525312 49525385 Eya1_peak_1268 85 . 6.85419 13.19086 8.54902 17 chr13 55211971 55212393 Eya1_peak_1108 85 . 6.85419 13.19086 8.54902 212 chr12 116485647 116485807 Eya1_peak_1025 85 . 6.85419 13.19086 8.54902 79 chr1 193036043 193036249 Eya1_peak_216 85 . 6.85419 13.19086 8.54902 117 chr1 192457671 192457793 Eya1_peak_214 85 . 6.85419 13.19086 8.54902 53 chr11 80613653 80613756 Eya1_peak_668 85 . 6.85419 13.19086 8.54902 63 chr11 54303182 54303314 Eya1_peak_540 85 . 6.85419 13.19086 8.54902 73 chr11 50291717 50292169 Eya1_peak_520 85 . 6.85419 13.19086 8.54902 285 chr8 117173844 117173919 Eya1_peak_3854 85 . 7.66643 13.14936 8.52183 26 chr5 135077664 135078172 Eya1_peak_3120 85 . 7.66643 13.14936 8.52183 409 chr9 82975081 82975497 Eya1_peak_4035 85 . 7.94442 13.13190 8.50554 227 chr8 93748861 93748947 Eya1_peak_3802 85 . 7.94442 13.13190 8.50554 38 chr4 47353297 47353482 Eya1_peak_2659 85 . 7.94442 13.13190 8.50554 63 chr3 119783116 119783247 Eya1_peak_2556 85 . 7.94442 13.13190 8.50554 59 chr19 38558972 38559076 Eya1_peak_2025 85 . 7.94442 13.13190 8.50554 42 chr19 23273487 23273739 Eya1_peak_2010 85 . 7.94442 13.13190 8.50554 59 chr18 31609702 31609821 Eya1_peak_1848 85 . 7.94442 13.13190 8.50554 57 chr1 59913093 59913286 Eya1_peak_56 85 . 7.94442 13.13190 8.50554 133 chr15 74382668 74382810 Eya1_peak_1398 85 . 7.94442 13.13190 8.50554 75 chr1 35017600 35017692 Eya1_peak_22 85 . 7.94442 13.13190 8.50554 40 chr12 29465326 29465463 Eya1_peak_885 85 . 7.94442 13.13190 8.50554 84 chr11 34448045 34448189 Eya1_peak_500 85 . 7.94442 13.13190 8.50554 58 chr11 29547432 29547779 Eya1_peak_483 85 . 7.94442 13.13190 8.50554 208 chr16 17891363 17891585 Eya1_peak_1531 84 . 7.64216 13.11098 8.49328 35 chr11 74723532 74723803 Eya1_peak_621 84 . 7.64216 13.11098 8.49328 113 chr11 69996368 69996918 Eya1_peak_600 84 . 7.64216 13.11098 8.49328 313 chr7 97579974 97580121 Eya1_peak_3546 84 . 7.91992 13.09354 8.47873 51 chr2 60125184 60125318 Eya1_peak_2175 84 . 7.34556 13.09598 8.47873 31 chr19 21272683 21272927 Eya1_peak_2007 84 . 7.91992 13.09354 8.47873 191 chr11 77687053 77687192 Eya1_peak_643 84 . 7.34556 13.09598 8.47873 96 chr11 72494157 72494244 Eya1_peak_612 84 . 7.34556 13.09598 8.47873 30 chr1 16519429 16519505 Eya1_peak_12 84 . 7.91992 13.09354 8.47873 31 chr8 72135396 72135757 Eya1_peak_3753 84 . 7.61805 13.07283 8.45909 16 chr8 109737419 109737675 Eya1_peak_3842 84 . 7.61805 13.07283 8.45909 68 chr7 124989614 124989700 Eya1_peak_3611 84 . 7.61805 13.07283 8.45909 41 chr5 88721343 88721472 Eya1_peak_2990 84 . 7.61805 13.07283 8.45909 86 chr5 140218058 140218151 Eya1_peak_3150 84 . 7.61805 13.07283 8.45909 47 chr4 33248417 33248511 Eya1_peak_2627 84 . 7.61805 13.07283 8.45909 34 chr4 103214732 103214988 Eya1_peak_2712 84 . 7.61805 13.07283 8.45909 107 chr2 112379250 112379454 Eya1_peak_2253 84 . 7.61805 13.07283 8.45909 57 chr18 31759619 31759757 Eya1_peak_1850 84 . 7.61805 13.07283 8.45909 72 chr17 66101293 66101408 Eya1_peak_1776 84 . 7.61805 13.07283 8.45909 60 chr17 28621900 28622037 Eya1_peak_1672 84 . 7.61805 13.07283 8.45909 79 chr16 96127297 96127613 Eya1_peak_1612 84 . 7.61805 13.07283 8.45909 61 chr12 54738493 54738566 Eya1_peak_902 84 . 7.61805 13.07283 8.45909 59 chr11 97187537 97187867 Eya1_peak_731 84 . 7.61805 13.07283 8.45909 295 chr11 69996994 69997077 Eya1_peak_601 84 . 7.61805 13.07283 8.45909 64 chr7 121034528 121035015 Eya1_peak_3597 84 . 7.89251 13.05065 8.44125 427 chr16 13667999 13668095 Eya1_peak_1516 84 . 7.89251 13.05065 8.44125 56 chr2 93900115 93900248 Eya1_peak_2231 84 . 7.59410 13.03491 8.42681 69 chr2 121413993 121414351 Eya1_peak_2271 84 . 7.59410 13.03491 8.42681 251 chr19 45998456 45998553 Eya1_peak_2045 84 . 7.59410 13.03491 8.42681 40 chr16 94570305 94570511 Eya1_peak_1604 84 . 7.59410 13.03491 8.42681 103 chr13 94789039 94789148 Eya1_peak_1166 84 . 7.59410 13.03491 8.42681 67 chr10 7681141 7681697 Eya1_peak_226 84 . 7.59410 13.03491 8.42681 245 chr7 70359126 70359261 Eya1_peak_3513 84 . 7.86530 13.00806 8.40142 36 chr2 18064193 18064394 Eya1_peak_2078 84 . 7.86530 13.00806 8.40142 150 chr5 99978190 99978467 Eya1_peak_3001 83 . 7.57029 12.99721 8.39123 109 chr11 102318702 102318920 Eya1_peak_767 83 . 7.26185 12.96045 8.35585 150 chr8 89042102 89042228 Eya1_peak_3798 83 . 7.54663 12.95974 8.35519 37 chr11 96004659 96004998 Eya1_peak_722 83 . 7.54663 12.95974 8.35519 251 chr15 79690983 79691142 Eya1_peak_1421 83 . 7.52312 12.92249 8.31941 113 chr2 102400624 102400913 Eya1_peak_2238 82 . 7.49976 12.88545 8.28395 102 chr11 54866479 54866893 Eya1_peak_544 82 . 7.49976 12.88545 8.28395 162 chr11 120572573 120572682 Eya1_peak_849 82 . 7.49976 12.88545 8.28395 54 chr3 96172578 96172846 Eya1_peak_2517 82 . 7.78476 12.88204 8.28108 13 chr2 65619924 65620011 Eya1_peak_2180 82 . 7.78476 12.88204 8.28108 37 chr12 100268159 100268239 Eya1_peak_987 82 . 6.93254 12.87234 8.27220 54 chr4 46451360 46451477 Eya1_peak_2655 82 . 7.47654 12.84863 8.24920 83 chr17 33972751 33972903 Eya1_peak_1695 82 . 7.47654 12.84863 8.24920 84 sort: write failed: 'standard output': Broken pipe sort: write error
In [17]:
cat Eya1_peaks.narrowPeak | wc -l
4164
In [33]:
cat Eya1_peaks.narrowPeak | sort -k9 -g -r | head -1000 > Eya1.chipseq_top1000.narrowpeak
sort: write failed: 'standard output': Broken pipe sort: write error
In [37]:
cat Eya1.chipseq_top1000.narrowpeak | wc -l
1000
In [40]:
cat Eya1.chipseq_top1000.narrowpeak | head -5
chr9 21950193 21950730 Eya1_peak_3907 1617 . 50.25843 171.22057 161.78474 344 chr15 72568544 72568871 Eya1_peak_1391 1436 . 42.95110 151.40498 143.65936 191 chr13 54970758 54971192 Eya1_peak_1104 1322 . 42.12254 139.63551 132.26416 294 chr12 42972811 42973228 Eya1_peak_893 1307 . 29.34931 138.06731 130.72491 148 chr2 34090652 34090884 Eya1_peak_2140 1264 . 40.58866 133.59843 126.41547 114 cat: write error: Broken pipe
Open the Eya1_peaks.narrowPeak file in IGV. The called peak in the REST.
Genome-wide ChIP-seq peaks¶
In [25]:
cat Eya1_peaks.narrowPeak | head
chr1 3670709 3670908 Eya1_peak_1 107 . 8.87783 15.54125 10.72335 128 chr1 4857782 4858014 Eya1_peak_2 108 . 8.35876 15.70195 10.87493 130 chr1 4858153 4858226 Eya1_peak_3 28 . 4.57189 6.68330 2.80234 64 chr1 5022813 5022938 Eya1_peak_4 94 . 7.18023 14.21410 9.49742 59 chr1 8123236 8123343 Eya1_peak_5 207 . 12.61147 26.03038 20.74978 55 chr1 9943673 9943778 Eya1_peak_6 33 . 5.17786 7.29091 3.32999 67 chr1 10037746 10037896 Eya1_peak_7 51 . 6.36931 9.45234 5.19167 33 chr1 10232651 10232724 Eya1_peak_8 33 . 5.42408 7.32244 3.35586 44 chr1 10232850 10233015 Eya1_peak_9 42 . 5.93520 8.42761 4.29727 31 chr1 13373303 13373399 Eya1_peak_10 35 . 5.59359 7.57307 3.56114 24 cat: write error: Broken pipe
In [26]:
cat Eya1_peaks.narrowPeak | cut -f 1-3 > Eya1_peaks.bed
In [27]:
head Eya1_peaks.bed
chr1 3670709 3670908 chr1 4857782 4858014 chr1 4858153 4858226 chr1 5022813 5022938 chr1 8123236 8123343 chr1 9943673 9943778 chr1 10037746 10037896 chr1 10232651 10232724 chr1 10232850 10233015 chr1 13373303 13373399
In [42]:
computeMatrix reference-point \
-S ChIP_Eya1.bw \
-R Eya1_peaks.bed \
--referencePoint center \
-a 1000 \
-b 1000 \
--binSize 5 \
-out Eya1.tab.gz
#-S: input file
#-R: reference file
#-a -b: choose how broad: each side of the centered of my file
# If this is full=> enlarge
#binSize 5: take every 5 nucleotides calculated the avg of my bigwig of the sum fit in the matrix
In [43]:
plotHeatmap \
-m Eya1.tab.gz \
-out Eya1_peaks.png \
--heatmapHeight 15 \
--refPointLabel peak.center \
--regionsLabel peaks \
--plotTitle 'ChIP-seq signal'
heatmap show peaks distribution within 2kb around the TSS
There is a big difference in the peak height among the all peaks
Motif Analysis¶
De novo motif discovery¶
Fetch FASTA sequences of the peaks from UCSC. Upload "Eya1_peaks.narrowPeak" file
Run RSAT peak-motifs
The most significant motif is REST DNA-binding motif(same result as paper)
REST DNA-binding motif belongs to zinc-finger.\ https://www.uniprot.org/uniprotkb/Q8VIG1/entry
REST Uniport
Eya1 don't have DNA binding activity. => Eya1 direct or indirect interacting with REST forming protein complexes bind at REST recognition sequences\
https://www.uniprot.org/uniprotkb/P97767/entry
Eya1 Uniprot
Create a BED file with only the DIRECT peaks = peaks with the REST motif¶
In [46]:
cat peak-motifs_dyads_m2dyads_m2_sites.tab | grep -v ";" | grep -v '#' | head
mm10_chr1_3670710_3670908_+ site dyads_m2dyads_m2 D 16 37 GAGCTGTCCTCGGTGCTGAAAT 19.4 mm10_chr1_5022814_5022938_+ site dyads_m2dyads_m2 D 31 52 GCACTCTCCAGGGTCCTGACGG 12.6 mm10_chr1_8123237_8123343_+ site dyads_m2dyads_m2 D 19 40 CCATTGACGCTGGTGCTGAAAT 9.2 mm10_chr1_34579663_34579736_+ site dyads_m2dyads_m2 D -24 -3 GAGCTGGCCGTGGTGCTGACGC 16.6 mm10_chr1_35017601_35017692_+ site dyads_m2dyads_m2 R 15 36 TCGCTGTCCGGGGTACTGATTT 16.4 mm10_chr1_37218520_37218691_+ site dyads_m2dyads_m2 D -36 -15 CCGCAGCCCACGGTGCTGAAAC 11.0 mm10_chr1_38939742_38939850_+ site dyads_m2dyads_m2 D -12 9 ACGCTGTCCACGGTGCTGACCG 17.9 mm10_chr1_56839045_56839203_+ site dyads_m2dyads_m2 D -36 -15 GTCCTGTCCATGGTACTGAAAT 20.7 mm10_chr1_63614753_63614856_+ site dyads_m2dyads_m2 R -8 13 GTGCTGTCCGGGGTGCTGAAGT 18.8 mm10_chr1_64158927_64159059_+ site dyads_m2dyads_m2 R -49 -28 GCTCTGTCCATGGTCCTGACTC 18.3 grep: write error: Broken pipe
In [47]:
cat peak-motifs_dyads_m2dyads_m2_sites.tab | grep -v ";" | grep -v '#' | cut -f 1 | tr "_" "\t" | cut -f 2-4 | head
chr1 3670710 3670908 chr1 5022814 5022938 chr1 8123237 8123343 chr1 34579663 34579736 chr1 35017601 35017692 chr1 37218520 37218691 chr1 38939742 38939850 chr1 56839045 56839203 chr1 63614753 63614856 chr1 64158927 64159059 cut: write error: Broken pipe
In [48]:
cat peak-motifs_dyads_m2dyads_m2_sites.tab | grep -v ";" | grep -v '#' | cut -f 1 | tr "_" "\t" | cut -f 2-4 > Eya1_peaks-with-motif-RSAT.bed
In [50]:
cat Eya1_peaks-with-motif-RSAT.bed
chr1 3670710 3670908 chr1 5022814 5022938 chr1 8123237 8123343 chr1 34579663 34579736 chr1 35017601 35017692 chr1 37218520 37218691 chr1 38939742 38939850 chr1 56839045 56839203 chr1 63614753 63614856 chr1 64158927 64159059 chr1 70725722 70725836 chr1 72537069 72537240 chr1 74858138 74858319 chr1 74891633 74891795 chr1 75263097 75263292 chr1 75277344 75277424 chr1 84696319 84696436 chr1 90028489 90028604 chr1 90028489 90028604 chr1 90028489 90028604 chr1 90028489 90028604 chr1 93272617 93272762 chr1 99772343 99772459 chr1 120331986 120332093 chr1 120390483 120390592 chr1 127496888 127497019 chr1 134664962 134665103 chr1 152956323 152956491 chr1 155594281 155594376 chr1 158019287 158019398 chr1 159524228 159524358 chr1 159621427 159621554 chr1 159702167 159702307 chr1 167079656 167079740 chr1 167123707 167123798 chr1 167187922 167188027 chr1 173361729 173361968 chr1 173361729 173361968 chr1 176697238 176697317 chr1 192457672 192457793 chr1 192472443 192472628 chr1 193036044 193036249 chr1 193738991 193739063 chr10 5639266 5639357 chr10 6788820 6788922 chr10 11081595 11081712 chr10 39967695 39967810 chr10 40961494 40961625 chr10 41071876 41071989 chr10 45483377 45483462 chr10 45546998 45547078 chr10 60914532 60914664 chr10 62138164 62138285 chr10 70598412 70598511 chr10 71403718 71403833 chr10 71428394 71428502 chr10 76958349 76958430 chr10 76978198 76978287 chr10 79718076 79718250 chr10 80748722 80748926 chr10 81477669 81477831 chr10 89224655 89224792 chr10 90376747 90376830 chr10 90823555 90823711 chr10 90827074 90827171 chr10 90881001 90881087 chr10 94305645 94305759 chr10 110676638 110676790 chr10 116019305 116019426 chr10 119705488 119705586 chr10 126625614 126625701 chr10 126681029 126681354 chr10 126681029 126681354 chr10 126681029 126681354 chr10 126681029 126681354 chr10 126681029 126681354 chr10 126681029 126681354 chr10 126681029 126681354 chr10 126681029 126681354 chr11 3153742 3153926 chr11 3774705 3774885 chr11 4076791 4076896 chr11 4750372 4750579 chr11 4763733 4763837 chr11 4949327 4949562 chr11 6016491 6016608 chr11 33680217 33680365 chr11 33787450 33787628 chr11 34448046 34448189 chr11 35798960 35799121 chr11 35798960 35799121 chr11 36090293 36090410 chr11 36396433 36396567 chr11 41999617 41999713 chr11 48012993 48013098 chr11 48696466 48696591 chr11 54303183 54303314 chr11 54343856 54343982 chr11 55607774 55608073 chr11 55897638 55897811 chr11 56812249 56812393 chr11 57434299 57434411 chr11 66259010 66259091 chr11 71389716 71389801 chr11 71937241 71937369 chr11 72113451 72113552 chr11 72494158 72494244 chr11 72607941 72608230 chr11 74619245 74619433 chr11 75173489 75173618 chr11 77930845 77931116 chr11 78496010 78496134 chr11 78952633 78952713 chr11 79593696 79593768 chr11 80312747 80312819 chr11 81005976 81006074 chr11 81115801 81115945 chr11 81194030 81194109 chr11 81966911 81966984 chr11 82313251 82313387 chr11 82371713 82371850 chr11 82514891 82515002 chr11 83417207 83417312 chr11 83421429 83421554 chr11 84662129 84662247 chr11 84724270 84724380 chr11 84729359 84729474 chr11 87921111 87921238 chr11 87957133 87957328 chr11 88047786 88048289 chr11 93097151 93097230 chr11 97078907 97079000 chr11 98314192 98314325 chr11 98324123 98324254 chr11 100203590 100203746 chr11 100758920 100759198 chr11 101602625 101602774 chr11 102393331 102393560 chr11 103656674 103656822 chr11 103920709 103921013 chr11 103920709 103921013 chr11 104053377 104053512 chr11 104114854 104114970 chr11 104198020 104198141 chr11 107817341 107817443 chr11 114652620 114652754 chr11 115052278 115052540 chr11 115052278 115052540 chr11 116920917 116921006 chr11 117873060 117873259 chr11 118584818 118585200 chr11 118584818 118585200 chr11 118584818 118585200 chr11 118584818 118585200 chr11 118603279 118603390 chr11 118659411 118659517 chr12 3955551 3955646 chr12 5111488 5111569 chr12 5717648 5717738 chr12 8099976 8100084 chr12 28831171 28831271 chr12 29465327 29465463 chr12 33084806 33084926 chr12 47252478 47252556 chr12 52504253 52504671 chr12 70347181 70347333 chr12 72422823 72422913 chr12 81206309 81206435 chr12 81776303 81776375 chr12 84698612 84698781 chr12 86547928 86548050 chr12 86983590 86983730 chr12 86994361 86994448 chr12 88709455 88709575 chr12 92040611 92040719 chr12 99041727 99041844 chr12 100268160 100268239 chr12 102550608 102550779 chr12 102555086 102555314 chr12 102949729 102949830 chr12 105266242 105266380 chr12 105266242 105266380 chr12 105322218 105322521 chr12 105322218 105322521 chr12 105322218 105322521 chr12 105322218 105322521 chr12 106115159 106115318 chr12 106633219 106633338 chr12 107464874 107464974 chr12 108994781 108994927 chr12 112141407 112141544 chr12 112511239 112511343 chr12 113188124 113188230 chr13 22035883 22036035 chr13 23990957 23991111 chr13 25269143 25269418 chr13 42447111 42447197 chr13 42711669 42711814 chr13 46097094 46097222 chr13 53948188 53948311 chr13 54260413 54260488 chr13 54371707 54371805 chr13 54749475 54749613 chr13 54750798 54751180 chr13 54750798 54751180 chr13 54758488 54758573 chr13 54876696 54876781 chr13 54945434 54945584 chr13 54970759 54971192 chr13 56895534 56895658 chr13 57867715 57867791 chr13 58663436 58663596 chr13 69896674 69896746 chr13 72902707 72902799 chr13 94878449 94878525 chr13 99564494 99564605 chr13 99900548 99900724 chr13 100210559 100210856 chr13 100210559 100210856 chr13 105442715 105442844 chr13 107419488 107419610 chr13 117604260 117604358 chr14 12530303 12530440 chr14 12823964 12824038 chr14 16365377 16365978 chr14 20093659 20093738 chr14 29657149 29657299 chr14 32321745 32322035 chr14 32597331 32597466 chr14 34867425 34867526 chr14 37016043 37016212 chr14 37068650 37068846 chr14 51985310 51985466 chr14 63681556 63681840 chr14 63681556 63681840 chr14 63681556 63681840 chr14 63713050 63713362 chr14 63713050 63713362 chr14 63713050 63713362 chr14 64568661 64568878 chr14 66161494 66161584 chr14 66909854 66909969 chr14 68125672 68125796 chr14 75366894 75367015 chr14 77195461 77195546 chr14 79769759 79769951 chr14 79785518 79785639 chr14 80157118 80157246 chr14 80215913 80216097 chr14 80257220 80257330 chr14 103536519 103536593 chr14 104453992 104454087 chr14 108913802 108914035 chr15 25118126 25118232 chr15 26309752 26309933 chr15 27655141 27655234 chr15 28823680 28823819 chr15 30913495 30913595 chr15 72201012 72201104 chr15 72568545 72568871 chr15 72568545 72568871 chr15 72568545 72568871 chr15 72568545 72568871 chr15 72689745 72690132 chr15 73026827 73027022 chr15 74076017 74076321 chr15 74076017 74076321 chr15 74382669 74382810 chr15 74549584 74549683 chr15 76521888 76522503 chr15 76521888 76522503 chr15 76722326 76722450 chr15 78066633 78066758 chr15 78119784 78120090 chr15 78119784 78120090 chr15 78153249 78153321 chr15 79791636 79791834 chr15 80203515 80203647 chr15 80277768 80277892 chr15 82921206 82921352 chr15 83879985 83880068 chr15 83924821 83924920 chr15 84086473 84086599 chr15 84109067 84109254 chr15 84829445 84829795 chr15 84829445 84829795 chr15 84829445 84829795 chr15 84965683 84965843 chr15 86544203 86544369 chr15 86932808 86932930 chr15 87887165 87887242 chr15 88325296 88325368 chr15 89150197 89150315 chr15 96460651 96460796 chr15 101473073 101473202 chr15 101879893 101880025 chr16 5765283 5765409 chr16 8914355 8914447 chr16 9836670 9836762 chr16 10501955 10502129 chr16 12359233 12359356 chr16 23890282 23890385 chr16 23890282 23890385 chr16 34400466 34400607 chr16 35302507 35303112 chr16 35302507 35303112 chr16 39985142 39985250 chr16 62758480 62758601 chr16 62758480 62758601 chr16 89071187 89071259 chr16 91011567 91011667 chr16 94972576 94972698 chr16 97286890 97286989 chr17 6256457 6256643 chr17 6321825 6322006 chr17 6490668 6490839 chr17 7741125 7741260 chr17 9066781 9066892 chr17 11309999 11310100 chr17 25239678 25239883 chr17 25400557 25400717 chr17 25813615 25813805 chr17 25813615 25813805 chr17 27228669 27228818 chr17 27466781 27466908 chr17 28575545 28575734 chr17 29362151 29362243 chr17 30938814 30938892 chr17 33972752 33972903 chr17 33972752 33972903 chr17 35270105 35270255 chr17 46704615 46704743 chr17 65370188 65370305 chr17 69439315 69439460 chr17 69969144 69969247 chr17 72603210 72603409 chr17 73488012 73488159 chr17 74489616 74489750 chr17 83010983 83011137 chr17 83010983 83011137 chr17 84820740 84820865 chr17 87798526 87798678 chr17 91092802 91092976 chr18 20916236 20916364 chr18 25500580 25500731 chr18 25668105 25668408 chr18 25668105 25668408 chr18 25668105 25668408 chr18 25668105 25668408 chr18 25668105 25668408 chr18 25752877 25753035 chr18 31447124 31447263 chr18 31760171 31760350 chr18 35977608 35977731 chr18 36004726 36004901 chr18 38056481 38056573 chr18 38075458 38075672 chr18 42396151 42396368 chr18 63977173 63977328 chr18 64042670 64042829 chr18 64266566 64266682 chr18 66561052 66561213 chr18 70411116 70411244 chr18 74608258 74608333 chr18 77274358 77274452 chr18 77417641 77417764 chr18 82030207 82030311 chr19 4988971 4989348 chr19 4988971 4989348 chr19 4988971 4989348 chr19 4988971 4989348 chr19 4992514 4992661 chr19 6502709 6502895 chr19 10403191 10403441 chr19 10403191 10403441 chr19 22139294 22139436 chr19 28818398 28818542 chr19 30030697 30030894 chr19 35833125 35833289 chr19 38558973 38559076 chr19 41661112 41661246 chr19 42255858 42256209 chr19 42255858 42256209 chr19 42255858 42256209 chr19 42326041 42326167 chr19 42425337 42425481 chr19 42636762 42636890 chr19 44692486 44692627 chr19 45097978 45098097 chr19 45813859 45814038 chr19 47006444 47006633 chr19 47016609 47016760 chr19 48168454 48168548 chr19 60469021 60469130 chr2 19429102 19429235 chr2 24488797 24488869 chr2 24762019 24762151 chr2 25318879 25319146 chr2 26208195 26208359 chr2 27142535 27142630 chr2 28195125 28195226 chr2 28916127 28916366 chr2 28916127 28916366 chr2 29310113 29310204 chr2 29573697 29573853 chr2 31346213 31346375 chr2 33018084 33018377 chr2 33018084 33018377 chr2 34090653 34090884 chr2 34090653 34090884 chr2 38418041 38418332 chr2 38418041 38418332 chr2 43613686 43613824 chr2 49503772 49503852 chr2 65619925 65620011 chr2 70559665 70559781 chr2 79454294 79454427 chr2 91921279 91921406 chr2 92401272 92401451 chr2 92671845 92671931 chr2 93071777 93071900 chr2 93900116 93900248 chr2 94524684 94524781 chr2 104299333 104299426 chr2 109675986 109676095 chr2 109675986 109676095 chr2 125135863 125136059 chr2 129715790 129715958 chr2 132781745 132781971 chr2 136714190 136714441 chr2 136714190 136714441 chr2 143207327 143207442 chr2 143536639 143536733 chr2 143546890 143547023 chr2 146226686 146226805 chr2 153032234 153032552 chr2 153032234 153032552 chr2 154076392 154076499 chr2 155775684 155775849 chr2 156652958 156653099 chr2 156677011 156677161 chr2 156677011 156677161 chr2 157663727 157663873 chr2 157913187 157913670 chr2 157913187 157913670 chr2 157913187 157913670 chr2 157913187 157913670 chr2 157970789 157970940 chr2 158570516 158570602 chr2 158584724 158584892 chr2 162031749 162031852 chr2 162568861 162568951 chr2 163439325 163439404 chr2 163564808 163564883 chr2 163889529 163889648 chr2 164966519 164966693 chr2 164968565 164968847 chr2 164979887 164979984 chr2 165159193 165159287 chr2 165160595 165160713 chr2 165456855 165456944 chr2 172042194 172042371 chr2 172110847 172110963 chr2 172320989 172321167 chr2 178277339 178277447 chr2 178330167 178330283 chr2 178735198 178735363 chr2 179193799 179193992 chr2 179193799 179193992 chr2 179193799 179193992 chr2 179616048 179616178 chr2 180104446 180104659 chr2 180417827 180417975 chr2 180756016 180756195 chr2 180894493 180894587 chr2 181126252 181126325 chr2 181302111 181302304 chr2 181302111 181302304 chr3 8508197 8508289 chr3 19694585 19694718 chr3 27370243 27370442 chr3 31309005 31309146 chr3 68064923 68065004 chr3 80802945 80803070 chr3 82412563 82412651 chr3 87993580 87993708 chr3 88220951 88221124 chr3 89159264 89159459 chr3 89764408 89764587 chr3 91213401 91213576 chr3 99311031 99311115 chr3 103573909 103574051 chr3 105275376 105275513 chr3 105577888 105577960 chr3 105959121 105959208 chr3 106962642 106962724 chr3 114904086 114904296 chr3 118431460 118431649 chr3 123508056 123508277 chr3 141811524 141811654 chr3 152821319 152821453 chr3 153267556 153267657 chr3 154819851 154819959 chr4 14145577 14145715 chr4 21712176 21712488 chr4 32601240 32601381 chr4 41532576 41532679 chr4 41546059 41546187 chr4 41606936 41607028 chr4 42945215 42945303 chr4 44260460 44260599 chr4 44434731 44434828 chr4 44511812 44511959 chr4 44578713 44578854 chr4 46992962 46993103 chr4 62257085 62257219 chr4 68955763 68955896 chr4 87221698 87221826 chr4 88722072 88722269 chr4 89313630 89313752 chr4 91379642 91379731 chr4 101550801 101550881 chr4 103572054 103572216 chr4 103875699 103875848 chr4 110119538 110119653 chr4 115728848 115728989 chr4 115887034 115887108 chr4 117893530 117893660 chr4 120866403 120866559 chr4 120880860 120880952 chr4 124317180 124317369 chr4 124633417 124633556 chr4 124882441 124882530 chr4 125300596 125300847 chr4 125300596 125300847 chr4 125300596 125300847 chr4 125328941 125329079 chr4 125503020 125503098 chr4 125590608 125590770 chr4 125835364 125835501 chr4 126655448 126655657 chr4 126655448 126655657 chr4 127173607 127173795 chr4 127173607 127173795 chr4 127619950 127620180 chr4 127619950 127620180 chr4 127619950 127620180 chr4 127970280 127970407 chr4 128042768 128042895 chr4 128248844 128248957 chr4 128913953 128914066 chr4 129120918 129121245 chr4 131115342 131115587 chr4 131115342 131115587 chr4 131658047 131658174 chr4 134020694 134020964 chr4 134020694 134020964 chr4 136907187 136907333 chr4 136924580 136924844 chr4 136924580 136924844 chr4 137676186 137676333 chr4 138597876 138598053 chr4 139059695 139059859 chr4 140258966 140259346 chr4 140258966 140259346 chr4 140258966 140259346 chr4 140258966 140259346 chr4 140258966 140259346 chr4 140283502 140283714 chr4 140283502 140283714 chr4 140283502 140283714 chr4 140358225 140358382 chr4 147957271 147957376 chr4 148229756 148229958 chr4 148229756 148229958 chr4 148286817 148286918 chr4 148293340 148293553 chr4 151185896 151185986 chr4 151186525 151186729 chr4 151288931 151289470 chr4 151288931 151289470 chr4 151288931 151289470 chr4 151288931 151289470 chr4 151288931 151289470 chr4 151288931 151289470 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151604518 151605412 chr4 151759272 151759375 chr4 152287047 152287180 chr4 152424500 152424609 chr4 153189630 153189775 chr4 153357660 153357770 chr4 153679298 153679421 chr4 154466462 154466552 chr4 155018792 155018938 chr4 155397641 155397757 chr4 155859356 155859714 chr4 155859356 155859714 chr4 155859356 155859714 chr4 155859356 155859714 chr5 22236949 22237074 chr5 24357560 24357689 chr5 26535697 26535783 chr5 26894492 26894592 chr5 27052588 27052660 chr5 27366083 27366208 chr5 27737223 27737424 chr5 31815285 31815357 chr5 33438279 33438516 chr5 33438279 33438516 chr5 35531808 35531898 chr5 36836091 36836213 chr5 36896317 36896416 chr5 37009890 37010211 chr5 37009890 37010211 chr5 37009890 37010211 chr5 37009890 37010211 chr5 37131994 37132077 chr5 37243472 37243665 chr5 37257374 37257507 chr5 37557633 37557710 chr5 62483690 62483780 chr5 63689228 63689318 chr5 77265819 77266303 chr5 99707419 99707500 chr5 110558515 110558623 chr5 111901766 111901956 chr5 111987170 111987246 chr5 112718669 112718984 chr5 112718669 112718984 chr5 113292306 113292399 chr5 113407465 113407592 chr5 113564620 113564746 chr5 113716719 113716909 chr5 115946110 115946187 chr5 116154995 116155122 chr5 116518203 116518286 chr5 116545914 116546006 chr5 116554042 116554146 chr5 116591455 116591613 chr5 116714392 116714511 chr5 116829932 116830089 chr5 116829932 116830089 chr5 116914997 116915148 chr5 117264876 117264980 chr5 117844737 117844876 chr5 120424129 120424289 chr5 121009543 121009704 chr5 121068819 121068935 chr5 121926531 121926676 chr5 124148454 124148536 chr5 127192015 127192132 chr5 128348959 128349062 chr5 128879280 128879376 chr5 129287600 129287710 chr5 130363921 130364012 chr5 135742280 135742352 chr5 135843520 135843678 chr5 137030209 137030384 chr5 137031178 137031280 chr5 137031178 137031280 chr5 137135130 137135220 chr5 139979035 139979141 chr5 140218059 140218151 chr5 141985169 141985312 chr5 142694733 142694862 chr5 144491403 144491686 chr5 144491403 144491686 chr5 146360503 146360631 chr5 146644639 146644821 chr5 148071931 148072110 chr6 8948577 8948727 chr6 8957615 8957735 chr6 28982517 28982671 chr6 31307166 31307298 chr6 31717640 31717761 chr6 31883868 31883992 chr6 31885340 31885456 chr6 31885340 31885456 chr6 32710304 32710467 chr6 36378093 36378170 chr6 45059215 45059366 chr6 48137004 48137102 chr6 52713755 52714160 chr6 55108442 55108645 chr6 83927573 83927689 chr6 84365133 84365205 chr6 84674281 84674353 chr6 85498318 85498404 chr6 89070122 89070258 chr6 95223627 95223782 chr6 113193843 113194095 chr6 113282090 113282216 chr6 113843378 113843450 chr6 113852456 113852686 chr6 113881920 113882081 chr6 114087247 114087392 chr6 115178978 115179091 chr6 118001456 118001560 chr6 119233175 119233286 chr6 119320632 119320747 chr6 121473010 121473450 chr6 121473010 121473450 chr6 122659692 122659843 chr6 127767905 127768115 chr6 128469529 128469648 chr6 139010656 139010728 chr6 146437008 146437147 chr7 4178528 4178727 chr7 4178528 4178727 chr7 4830660 4830860 chr7 6410076 6410420 chr7 6410076 6410420 chr7 6410076 6410420 chr7 6410076 6410420 chr7 16147766 16147930 chr7 16183793 16183984 chr7 18951535 18951660 chr7 19573201 19573338 chr7 24359378 24359579 chr7 24359378 24359579 chr7 24727774 24727900 chr7 25146040 25146178 chr7 27396258 27396331 chr7 28263919 28264083 chr7 28505736 28505819 chr7 30346762 30346943 chr7 30434363 30434457 chr7 30484369 30484466 chr7 34702895 34703009 chr7 39455939 39456083 chr7 40762728 40762818 chr7 44335741 44335866 chr7 44593894 44594090 chr7 44770096 44770391 chr7 44770096 44770391 chr7 44770096 44770391 chr7 49910556 49910667 chr7 51621838 51621946 chr7 57592313 57592438 chr7 70360030 70360230 chr7 81493355 81493552 chr7 82625452 82625609 chr7 82625452 82625609 chr7 84085101 84085250 chr7 99648812 99648944 chr7 101438008 101438111 chr7 109129582 109129672 chr7 110701764 110701977 chr7 111081803 111082617 chr7 117021828 117021986 chr7 117636815 117636933 chr7 117636815 117636933 chr7 118001238 118001389 chr7 119111922 119112020 chr7 119356363 119356475 chr7 120426819 120426891 chr7 121391351 121391471 chr7 121596534 121596651 chr7 121730340 121730494 chr7 122670869 122671111 chr7 122670869 122671111 chr7 123235572 123235699 chr7 123503470 123503594 chr7 124199058 124199195 chr7 124742214 124742340 chr7 124989615 124989700 chr7 126825590 126825694 chr7 128231876 128231995 chr7 129469620 129469785 chr7 131245159 131245277 chr7 131917501 131917602 chr7 132060260 132060385 chr7 133511085 133511178 chr7 137945135 137945253 chr7 138084023 138084287 chr7 138084023 138084287 chr7 138084023 138084287 chr7 138084023 138084287 chr7 138084023 138084287 chr7 141973455 141973557 chr7 144160232 144160310 chr7 144294419 144294512 chr8 9309609 9309725 chr8 9635325 9635499 chr8 9635325 9635499 chr8 9769204 9769332 chr8 14072572 14072895 chr8 14072572 14072895 chr8 14072572 14072895 chr8 14072572 14072895 chr8 38747310 38747394 chr8 55754335 55754418 chr8 55940689 55940811 chr8 70885757 70885878 chr8 71483977 71484105 chr8 74851958 74852038 chr8 78431493 78431646 chr8 78438371 78438447 chr8 84454689 84454862 chr8 84471317 84471557 chr8 84947107 84947546 chr8 84947107 84947546 chr8 87087611 87087685 chr8 87700496 87700606 chr8 94482282 94482380 chr8 94800800 94800914 chr8 95028538 95028634 chr8 105291038 105291153 chr8 105693811 105693911 chr8 110196825 110196940 chr8 112128885 112129121 chr8 112128885 112129121 chr8 112404221 112404340 chr8 117173845 117173919 chr8 118951924 118951996 chr8 119164208 119164292 chr8 119258690 119258895 chr8 119258690 119258895 chr8 119258690 119258895 chr8 121736356 121736468 chr8 121761638 121761747 chr8 123414388 123414507 chr8 123891459 123891548 chr8 126404663 126404774 chr9 20813142 20813267 chr9 20857161 20857410 chr9 20857161 20857410 chr9 21950194 21950730 chr9 21950194 21950730 chr9 22053846 22053918 chr9 26727584 26727693 chr9 27308179 27308324 chr9 29146083 29146171 chr9 34837837 34837965 chr9 40269712 40269789 chr9 40801359 40801567 chr9 40873797 40873996 chr9 42652863 42652959 chr9 43698590 43698715 chr9 43934766 43934893 chr9 43959625 43959808 chr9 45710578 45710656 chr9 46642809 46642992 chr9 48898725 48898797 chr9 49341153 49341294 chr9 50029218 50029290 chr9 54271040 54271153 chr9 55026329 55026440 chr9 56738430 56738534 chr9 57468142 57468242 chr9 58060893 58061158 chr9 58841787 58841938 chr9 59578344 59578528 chr9 61484519 61484641 chr9 64624677 64624805 chr9 64666647 64666840 chr9 69856757 69856876 chr9 74868518 74868626 chr9 89737423 89737518 chr9 98234884 98234980 chr9 99218354 99218632 chr9 99563876 99564020 chr9 100023788 100023888 chr9 104569428 104569631 chr9 105272452 105272524 chr9 105893820 105893905 chr9 107381813 107381945 chr9 108825914 108825992 chr9 108826580 108827252 chr9 119149702 119149869 chr9 119389102 119389237 chr9 119706828 119706971 chr9 121791343 121791495 chr9 122006690 122006819 chrUn JH584304 4617 chrX 7795194 7795274 chrX 73869426 73869643 chrX 73869426 73869643 chrX 143904847 143904930
Position-Specific Scoring Matrix (PSSM) and track enrichment¶
Peaks correlate with other epigenomic data sets called tracks.\ i-cisTarget will test for enrichment of motifs, using a collection of databases of PSSMs, as well as tracks.\ Position-Specific Scoring Matrix = position weight matrix (PWM)
The most significantly motif was the REST (same result as RSAT database and paper)\
REST => transcriptional repressor that represses neuronal genes in non-neuronal tissues. It also found in undifferentiated neuronal progenitor cells.
Leading edge in i-cisTarget for the REST motif = directly bound regions¶
In [59]:
cat hocomoco__REST_MOUSE.H11MO.0.A.targets.bed | head
track name=hocomoco__REST_MOUSE.H11MO.0.A_candidate_targets description="" useScore=1 chr8 84454553 84454901 chr8:84454553-84454901 chr4 125328868 125329138 chr4:125328868-125329138 chr8 86425479 86425678 chr8:86425479-86425678 chrX 7795139 7795303 chrX:7795139-7795303 chr16 89071105 89071366 chr16:89071105-89071366 chr14 79785452 79785717 chr14:79785452-79785717 chr6 146437016 146437257 chr6:146437016-146437257 chr17 83010904 83011155 chr17:83010904-83011155 chr14 80157069 80157323 chr14:80157069-80157323
In [60]:
cat hocomoco__REST_MOUSE.H11MO.0.A.targets.bed | wc -l
672
672 peaks are in the leading edge, and the total peaks of Eya1 is 4164.\ Therefore, 16% of the input peaks contain a good match of the REST motif.
The Eya1 peaks is associated with transcriptional, posttranscriptional, translational regulation and histone modification.
- peaks with REST motif (Eya1_peaks-with-motif-RSAT.bed file)
The Eya1 peaks occupied in REST motif is related to synaptic transmission, ion transport and secretion.
- peaks with REST motif (Eya1_peaks-with-motif-iCisTarget.bed file)
The result is almost the same as the result of REST motif in RSAT database.
Genes related to REST (STRING)¶
Using STRING to identify which gene are ssociated with REST.
In [26]:
cat string_protein_annotations_REST.tsv | cut -f1 | head
#node Actl6a Actl6b Arid4a Arid4b Batf Bdnf Bptf Brms1 Btrc
In [27]:
cat string_protein_annotations_REST.tsv | cut -f 1 | grep -v '#' > REST-string-top100.txt
In [15]:
list=`cat REST-string-top100.txt`
Next step, find the common genes shown both in REST motif (Eya1_peaks-with-motif-RSAT) and REST in SRING database (REST-string-top100.txt).
In [16]:
for i in $list; do grep -w $i 1GREAT_REST_targets_regulation_of_membrane_potential.txt; done
unnamed Bdnf (+1341) unnamed Bdnf (+1341)
In [13]:
for i in $list; do grep -w $i 2GREAT_REST_modulation_of_synaptic_transmission.txt; done
unnamed Bdnf (+1341) unnamed Bdnf (+1341) unnamed Creb1 (-373816)
In [17]:
for i in $list; do grep -w $i 3GREAT_REST_targets_neuromuscular_process_controlling_balance.txt; done
In [18]:
for i in $list; do grep -w $i 4GREAT_REST_targets_cation_transport.txt; done
unnamed Rest (+570)
In [19]:
for i in $list; do grep -w $i 5GREAT_REST_targets_trans-synaptic_signaling.txt; done
unnamed Lin7c (-214812), Bdnf (+1341) unnamed Lin7c (-214812), Bdnf (+1341)
In [20]:
for i in $list; do grep -w $i 7GREAT_REST_targets_signal_release.txt; done
unnamed Neurod1 (+2390)
In [21]:
for i in $list; do grep -w $i 15GREAT_REST_targets_neurotransmitter_transport.txt; done
Few genes found => use 300 number of STRING
In [23]:
cat string_protein_annotations_REST_300.tsv | cut -f1 | head
#node Actl6a Actl6b Ar Arid4a Arid4b Ascl1 Batf Bdnf Bptf
In [28]:
cat string_protein_annotations_REST_300.tsv | cut -f 1 | grep -v '#' > REST-string-top300.txt
In [29]:
list=`cat REST-string-top300.txt`
In [30]:
for i in $list; do grep -w $i 1GREAT_REST_targets_regulation_of_membrane_potential.txt; done
unnamed Bdnf (+1341) unnamed Bdnf (+1341)
In [31]:
for i in $list; do grep -w $i 2GREAT_REST_modulation_of_synaptic_transmission.txt; done
unnamed Bdnf (+1341) unnamed Bdnf (+1341) unnamed Creb1 (-373816)
In [32]:
for i in $list; do grep -w $i 3GREAT_REST_targets_neuromuscular_process_controlling_balance.txt; done
In [33]:
for i in $list; do grep -w $i 4GREAT_REST_targets_cation_transport.txt; done
unnamed Rest (+570)
In [34]:
for i in $list; do grep -w $i 5GREAT_REST_targets_trans-synaptic_signaling.txt; done
unnamed Lin7c (-214812), Bdnf (+1341) unnamed Lin7c (-214812), Bdnf (+1341) unnamed Nrxn2 (+84071) unnamed Nrxn3 (-84989)
In [35]:
for i in $list; do grep -w $i 7GREAT_REST_targets_signal_release.txt; done
unnamed Neurod1 (+2390) unnamed Nrxn2 (+84071) unnamed Nrxn3 (-84989)
In [36]:
for i in $list; do grep -w $i 15GREAT_REST_targets_neurotransmitter_transport.txt; done
unnamed Nrxn2 (+84071) unnamed Nrxn3 (-84989)
Only 7 genes shown both in REST-related STRING database and REST-motif GREAT database. \ => these genes are both ChIP-seq peak nearby (<50kb) and somehow associated with REST.
Comparison of STRING and iRegulon¶
Analze with iRegulon to see the motif and targets are already connected
In [37]:
list=`cat REST-string-top300.txt`
In [38]:
for i in $list; do grep -w $i REST_target_gene_iRegulon_geneID.txt; done
Nr2e1 21907 Srrm4 68955
Only 2 genes are found => the target gene of REST are few reported => we can validate these genes whether they are directly bound with REST by implementing experiments to proof.
Nr2e1 => an orphan receptor involved in the regulation of retinal development and essential for vision\ Srrm4 => required for neural cell differentiation.
Conclusion¶
Two strategy: De novo motif discovery (RSAT peak-motifs) and enrichment of motifs (i-cis Target) both identified recognition site is GCTGTCCATGGTGCTGAA which belongs to REST motif. The result point out that Eya1 does not directly bind to DNA and must through its interacting partners such as REST(zinc-finger transcriptional repressor) or other co-regulator to activate or repress gene expression. The result of finding REST is the same as when utilizing iRegulon of bulk RNA-seq analysis.
GREAT database indicate that Eya1-occupied REST motif peaks are gene about synaptic transmission, ion transport and secretion, all about neuron, but no nephron-related term was enriched. Interestingly, the author also use Six2 Chip analysis and overlap of Eya1 peaks and Six2 peaks. They both identify REST recognition sequences, suggesting that Eya1 cooperate with Six2 through REST transcription factor to regulate gene expression and further maintain the NPSc identity.